ClinVar Genomic variation as it relates to human health
NM_004168.4(SDHA):c.91C>T (p.Arg31Ter)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_004168.4(SDHA):c.91C>T (p.Arg31Ter)
Variation ID: 142601 Accession: VCV000142601.77
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5p15.33 5: 223509 (GRCh38) [ NCBI UCSC ] 5: 223624 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 25, 2014 Apr 15, 2024 Feb 6, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_004168.4:c.91C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_004159.2:p.Arg31Ter nonsense NM_001294332.2:c.91C>T NP_001281261.1:p.Arg31Ter nonsense NM_001330758.2:c.91C>T NP_001317687.1:p.Arg31Ter nonsense NC_000005.10:g.223509C>T NC_000005.9:g.223624C>T NG_012339.1:g.10269C>T LRG_315:g.10269C>T LRG_315t1:c.91C>T LRG_315p1:p.Arg31Ter - Protein change
- R31*
- Other names
- p.R31X
- Canonical SPDI
- NC_000005.10:223508:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
Trans-Omics for Precision Medicine (TOPMed) 0.00019
The Genome Aggregation Database (gnomAD), exomes 0.00020
The Genome Aggregation Database (gnomAD) 0.00025
Exome Aggregation Consortium (ExAC) 0.00016
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SDHA | - | - |
GRCh38 GRCh37 |
2620 | 2776 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Apr 16, 2022 | RCV000131808.14 | |
Pathogenic/Likely pathogenic (10) |
criteria provided, multiple submitters, no conflicts
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Apr 24, 2023 | RCV000148026.25 | |
Likely pathogenic (1) |
no assertion criteria provided
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- | RCV000170328.9 | |
Pathogenic (14) |
criteria provided, multiple submitters, no conflicts
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Feb 6, 2024 | RCV000413945.46 | |
Pathogenic (2) |
criteria provided, single submitter
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Jan 31, 2024 | RCV000627791.17 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 24, 2017 | RCV000722034.10 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jan 6, 2020 | RCV001089554.13 | |
Pathogenic (1) |
no assertion criteria provided
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Sep 1, 2020 | RCV001257553.9 | |
Pathogenic (1) |
no assertion criteria provided
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Aug 4, 2022 | RCV001762318.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 1, 2021 | RCV001799624.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 2, 2021 | RCV002478402.8 | |
Pathogenic (1) |
criteria provided, single submitter
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- | RCV003335126.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 15, 2023 | RCV003330507.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 2, 2023 | RCV003474779.1 | |
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Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Nov 09, 2017)
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criteria provided, single submitter
Method: research
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Paragangliomas 5
Affected status: unknown
Allele origin:
unknown
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HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology
Study: CSER-HudsonAlpha
Accession: SCV000677113.1 First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
Number of individuals with the variant: 1
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Pathogenic
(Jun 06, 2018)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Department of Pediatrics, Memorial Sloan Kettering Cancer Center
Accession: SCV000778378.1
First in ClinVar: May 26, 2018 Last updated: May 26, 2018 |
Comment:
This mutation was observed in 9 patients in our cancer study. Additional supporting evidence for this mutation contributing to the specific cancers manifested by patients … (more)
This mutation was observed in 9 patients in our cancer study. Additional supporting evidence for this mutation contributing to the specific cancers manifested by patients in our cohort, were in the settings of GIST and neuroblastoma. For patients with other cancer types in our cohort, this alteration is suggestive of an independent risk factor for cancers than experienced by the patients. (less)
Number of individuals with the variant: 9
Sex: mixed
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Pathogenic
(Jan 06, 2020)
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criteria provided, single submitter
Method: clinical testing
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Leigh syndrome
Affected status: yes
Allele origin:
unknown
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Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Accession: SCV001244791.2
First in ClinVar: May 04, 2020 Last updated: Sep 19, 2020 |
Comment:
A heterozygous nonsense variant, NM_004168.2(SDHA):c.91C>T, has been identified in exon 2 of 15 of the SDHA gene. The variant is predicted to result in a … (more)
A heterozygous nonsense variant, NM_004168.2(SDHA):c.91C>T, has been identified in exon 2 of 15 of the SDHA gene. The variant is predicted to result in a premature stop codon at position 31 of the protein (NP_004159.2(SDHA):p.(Arg31*)), likely causing nonsense-mediated decay. This variant is predicted to result in loss of protein function either through truncation (including FAD-dependent oxidoreductase 2 domain and fumerate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain) or nonsense-mediated decay, which is a reported mechanism of pathogenicity for this gene. The variant is present in the gnomAD database at a frequency of 0.0209%. The variant has been previously described as pathogenic in a compound heterozygous state in one patient with Leighsyndrome (Renkema GH. et al., (2015)). Functional analysis demonstrated a partial reduction in protein and almost complete loss of complex II activity (Renkema GH. et al., (2015)). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC. (less)
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Pathogenic
(Jan 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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Leigh syndrome
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001370210.2
First in ClinVar: Jul 06, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PP4,PP5.
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Likely pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Affected status: yes
Allele origin:
germline
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Genomics England Pilot Project, Genomics England
Accession: SCV001760160.1
First in ClinVar: Jul 31, 2021 Last updated: Jul 31, 2021 |
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Pathogenic
(Oct 01, 2021)
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criteria provided, single submitter
Method: research
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Gastrointestinal stromal tumor
Affected status: yes
Allele origin:
germline
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“Giorgio Prodi” Cancer Research Center, University of Bologna
Accession: SCV002026125.1
First in ClinVar: Jan 03, 2022 Last updated: Jan 03, 2022 |
Number of individuals with the variant: 1
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Pathogenic
(Nov 29, 2021)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Affected status: yes
Allele origin:
unknown
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Institute of Human Genetics, University of Leipzig Medical Center
Accession: SCV002044344.1
First in ClinVar: Jan 03, 2022 Last updated: Jan 03, 2022 |
Comment:
_x000D_ Criteria applied: PVS1, PS4
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Pathogenic
(Dec 09, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not provided
Affected status: yes
Allele origin:
germline
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AiLife Diagnostics, AiLife Diagnostics
Accession: SCV002502762.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
Number of individuals with the variant: 3
Secondary finding: no
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Pathogenic
(Mar 25, 2021)
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criteria provided, single submitter
Method: curation
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Sema4, Sema4
Accession: SCV002527776.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022 |
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Pathogenic
(Apr 29, 2022)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Affected status: yes
Allele origin:
germline
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MGZ Medical Genetics Center
Accession: SCV002579899.1
First in ClinVar: Oct 15, 2022 Last updated: Oct 15, 2022 |
Number of individuals with the variant: 3
Sex: male
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Pathogenic
(Apr 16, 2022)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000186863.7
First in ClinVar: Aug 06, 2014 Last updated: Nov 29, 2022 |
Comment:
The p.R31* pathogenic mutation (also known as c.91C>T), located in coding exon 2 of the SDHA gene, results from a C to T substitution at … (more)
The p.R31* pathogenic mutation (also known as c.91C>T), located in coding exon 2 of the SDHA gene, results from a C to T substitution at nucleotide position 91. This changes the amino acid from an arginine to a stop codon within coding exon 2. This mutation has been reported in multiple individuals diagnosed with isolated paraganglioma (Rattenberry E et al. J. Clin. Endocrinol. Metab. 2013 Jul;98:E1248-56; Bahougne T et al. Endocr. Relat. Cancer. 2017 Feb;24:L7-L11; Lussey-Lepoutre C et al. Clin. Cancer Res. 2016 Mar;22:1120-9). This mutation was also detected in 2/692 (0.3%) Dutch controls, which suggests a low penetrance of paragangliomas in individuals with this mutation (Korpershoek E et al. J. Clin. Endocrinol. Metab. 2011 Sep;96:E1472-6). This alteration has also been reported in individuals with gastrointestinal stromal tumors and pheochromocytomas, an individual with adrenocortical carcinoma, and an individual with SDHA-deficient renal cell carcinoma (Pantaleo MA et al. J. Natl. Cancer Inst. 2011 Jun;103:983-7; Wagner AJ et al. Mod. Pathol. 2013 Feb;26:289-94; Oudijk L et al. Mod. Pathol. 2013 Mar;26:456-63; Else T et al. Eur. J. Endocrinol. 2017 Nov;177:439-444; McEvoy CR et al. NPJ Precis Oncol. 2018 Mar;2:9; Dubard Gault M et al. Cold Spring Harb Mol Case Stud. 2018 08;4:(4); Tufton N et al. Endocr. Relat. Cancer. 2017 07;24:L43-L49). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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Pathogenic
(Jun 10, 2017)
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criteria provided, single submitter
Method: provider interpretation, clinical testing
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Paragangliomas 5
Affected status: no
Allele origin:
paternal
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Geisinger Autism and Developmental Medicine Institute, Geisinger Health System
Accession: SCV000804427.2
First in ClinVar: May 26, 2018 Last updated: Dec 11, 2022 |
Comment:
This 6 year old male with global developmental delays (at-risk for mild intellectual disability), ADHD, disruptive behavior, and mild overgrowth was found to carry a … (more)
This 6 year old male with global developmental delays (at-risk for mild intellectual disability), ADHD, disruptive behavior, and mild overgrowth was found to carry a paternally inherited nonsense variant in the SDHA gene. The R31X pathogenic variant in the SDHA gene has been reported previously in the heterozygous state in association with hereditary paraganglioma-pheochromocytoma syndrome (Korpershoek et al., 2011; Rattenberry et al., 2013; Batsis et al., 2016) and in individuals with gastrointestinal stromal tumors (Pantaleo et al., 2011; Wagner et al., 2013; Oudijk et al., 2013). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The patient does not yet show any signs of hereditary paraganglioma-pheochromocytoma syndrome. His father has not yet been formally evaluated, but he reports a history of hypertension. (less)
Observation 1:
Clinical Features:
Global developmental delay (present) , Attention deficit hyperactivity disorder (present) , Behavioral abnormality (present) , Overgrowth (present)
Age: 0-9 years
Sex: male
Secondary finding: yes
Testing laboratory: GeneDx
Date variant was reported to submitter: 2017-05-19
Testing laboratory interpretation: Pathogenic
Observation 2:
Number of individuals with the variant: 1
Clinical Features:
Global developmental delay (present) , Attention deficit hyperactivity disorder (present) , Behavioral abnormality (present) , Overgrowth (present)
Age: 0-9 years
Sex: male
Testing laboratory: GeneDx
Date variant was reported to submitter: 2017-05-19
Testing laboratory interpretation: Pathogenic
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Pathogenic
(Nov 07, 2022)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002556866.2
First in ClinVar: Aug 08, 2022 Last updated: Dec 17, 2022 |
Comment:
The SDHA c.91C>T variant is classified as Pathogenic (PVS1, PS4_Moderate, PS3) The SDHA c.91C>T variant is a single nucleotide change which is predicted to result … (more)
The SDHA c.91C>T variant is classified as Pathogenic (PVS1, PS4_Moderate, PS3) The SDHA c.91C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 31 (PVS1). This variant has been reported in multiple individuals with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad (PMID: 26173966), as well as non-PGL tumors (PMID: 21505157, 22955521, 23174939, 21752896, 23666964, 25494863, 26259135) (PS4_Moderate). Well-established functional studies show a deleterious effect of this variant (PMID:24781757) (PS3). The variant has been reported in dbSNP (rs142441643) and has been reported in population databases (gnomAD 37/152202, 0 homozygotes). The variant has been reported in the HGMD database as disease causing (CM114717) and as Pathogenic/Likely pathogenic by other diagnostic laboratories (ClinVar Variation ID: 142601). (less)
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Pathogenic
(Oct 27, 2015)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000677772.2
First in ClinVar: Dec 26, 2017 Last updated: Dec 24, 2022 |
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Pathogenic
(Oct 02, 2021)
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criteria provided, single submitter
Method: clinical testing
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Mitochondrial complex II deficiency, nuclear type 1
Dilated cardiomyopathy 1GG Paragangliomas 5 Neurodegeneration with ataxia and late-onset optic atrophy
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000893699.2
First in ClinVar: Mar 31, 2019 Last updated: Dec 31, 2022 |
|
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Pathogenic
(May 12, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000490791.6
First in ClinVar: Jan 09, 2017 Last updated: Mar 04, 2023 |
Comment:
Observed with a second SDHA variant on the opposite allele (in trans) in an individual with Leigh syndrome (Renkema 2015); Nonsense variant predicted to result … (more)
Observed with a second SDHA variant on the opposite allele (in trans) in an individual with Leigh syndrome (Renkema 2015); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Published functional studies demonstrate loss of protein expression (Dubard Gault 2018); This variant is associated with the following publications: (PMID: 31368675, 30854332, 25394176, 27171833, 23252569, 27604842, 28546994, 22974104, 30877234, 25525159, 24886695, 23612575, 25494863, 26259135, 23109135, 21505157, 23666964, 21752896, 27895137, 28819017, 22955521, 23174939, 30068732, 29978187, 26173966, 29625052, 26689913, 29177515, 28500238, 31169996, 29978154, 32581362, 31827275, 34308366, 31589614, 33372952, 33077847, 33960148, 33674644, 24781757) (less)
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Pathogenic
(Nov 03, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
germline
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Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
Accession: SCV002009952.3
First in ClinVar: Nov 06, 2021 Last updated: Jul 16, 2023 |
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Pathogenic
(Aug 15, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurodegeneration with ataxia and late-onset optic atrophy
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004039536.1
First in ClinVar: Oct 07, 2023 Last updated: Oct 07, 2023 |
Comment:
Variant summary: SDHA c.91C>T (p.Arg31X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: SDHA c.91C>T (p.Arg31X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Variants downstream of this position have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 0.0002 in 251180 control chromosomes (gnomAD). c.91C>T has been reported in the literature in multiple individuals affected with pheochromocytomas and paragangliomas, SSDH-deficient gastrointestinal stromal tumors and significant ataxia, with progressive cerebellar atrophy (examples: Korpershoek_ 2011, Panteleo_ 2022, Sturrock_ 2020). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 35059314, 21752896, 33960148). Twenty two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic (n=20)/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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SDHA-related disorders
Affected status: yes
Allele origin:
germline
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Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego
Accession: SCV004046374.1
First in ClinVar: Oct 21, 2023 Last updated: Oct 21, 2023 |
Comment:
This nonsense variant found in exon 2 of 15 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated … (more)
This nonsense variant found in exon 2 of 15 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been reported in multiple individuals with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad (PMID: 26173966), and non-PGL tumors (PMID: 21505157, 22955521, 23174939, 21752896, 23666964, 25494863, 26259135). This variant has also been reported as a compound heterozygous change in an individual diagnosed with autosomal-recessive complex II deficiency (PMID: 24781757). Functional studies showed that the presence of this variant caused reduced expression of SDHA protein and mitochondrial complex II enzyme activity (PMID: 24781757). Loss-of-function variants are an established mechanism of disease in SDHA-related disorders (HGMD, ClinVar database). The c.91C>T (p.Arg31Ter) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.021% (59/282590) and thus is presumed to be rare. Based on the available evidence, the c.91C>T (p.Arg31Ter) variant is classified as Pathogenic. (less)
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Pathogenic
(Apr 24, 2023)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004045363.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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Pathogenic
(Aug 02, 2023)
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criteria provided, single submitter
Method: clinical testing
|
Dilated cardiomyopathy 1GG
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004200605.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
|
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Pathogenic
(Dec 23, 2022)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV004220328.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
This nonsense variant causes the premature termination of SDHA protein synthesis. In the published literature, the variant has been reported in patients with paragangliomas, pheochromocytomas, … (more)
This nonsense variant causes the premature termination of SDHA protein synthesis. In the published literature, the variant has been reported in patients with paragangliomas, pheochromocytomas, and gastrointestinal stromal tumors (PMIDs: 26173966 (2016), 26490314 (2016), 25494863 (2015), 26259135 (2015), 23666964 (2013), 22955521 (2013), 23174939 (2013)). Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Mar 28, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Not provided
Affected status: unknown
Allele origin:
germline
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV004225835.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
PP1, PP4, PVS1
Number of individuals with the variant: 5
|
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Pathogenic
(Feb 06, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Accession: SCV004024961.2
First in ClinVar: Aug 19, 2023 Last updated: Feb 14, 2024 |
|
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Pathogenic
(Aug 24, 2017)
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criteria provided, single submitter
Method: clinical testing
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Pilocytic astrocytoma
Affected status: yes
Allele origin:
germline
|
St. Jude Molecular Pathology, St. Jude Children's Research Hospital
Accession: SCV000853211.1
First in ClinVar: Nov 25, 2018 Last updated: Nov 25, 2018 |
Comment:
This is a nonsense alteration in which a C is replaced by a T at coding nucleotide 91 and is predicted to change an Arginine … (more)
This is a nonsense alteration in which a C is replaced by a T at coding nucleotide 91 and is predicted to change an Arginine to a premature stop codon at amino acid codon 31. Classification criteria: PVS1, PS1, PP5. (less)
Sex: female
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Pathogenic
(May 21, 2018)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884500.1
First in ClinVar: Jan 09, 2017 Last updated: Jan 09, 2017 |
Comment:
The SDHA c.91C>T; p.Arg31Ter variant (rs142441643) is reported in the literature associated with disease in multiple patients. Genetic testing of a gastrointestinal stromal tumor (GIST) … (more)
The SDHA c.91C>T; p.Arg31Ter variant (rs142441643) is reported in the literature associated with disease in multiple patients. Genetic testing of a gastrointestinal stromal tumor (GIST) in a young adult patient identified the p.Arg31Ter variant in trans from another pathogenic variant (p.Arg589Trp); subsequent testing revealed that the p.Arg31Ter variant was germline whereas the p.Arg589Trp variant was detected only in the tumor (Pantaleo 2011). Another study of paragangliomas (PGL) and pheochromocytomas identified the p.Arg31Ter variant in four tumors (patients were heterozygous for germline p.Arg31Ter, whereas tumors showed loss-of-heterozygosity); however, the same variant was also identified in 0.3% of healthy controls (Korpershoek 2011). A number of other studies have reported the p.Arg31Ter variant in both PGL and non-PGL tumors, often with evidence of p.Arg31Ter as a germline variant in affected patients (Boikos 2016, Denes 2015, Else 2017, Lussey-Lepoutre 2016, Niemeijer 2015, Oudijk 2013, Rattenberry 2013, Wagner 2013). Finally, p.Arg31Ter was also identified in trans from a germline p.Cys189Gly variant in a patient with multisystem mitochondrial disease (Renkema 2015). The p.Arg31Ter variant is classified as pathogenic by multiple laboratories in ClinVar (Variation ID: 142601). It is found in the general population databases with an overall allele frequency of 0.02% (58/276948 alleles) in the Genome Aggregation Database. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. However, pathogenic heterozygous SDHA variants have incomplete penetrance (Casey 2017) and the individual risk has yet to be determined. REFERENCES Boikos SA et al. Carney triad can be (rarely) associated with germline succinate dehydrogenase defects. Eur J Hum Genet. 2016 Apr;24(4):569-73. Casey RT et al. SDHA related tumorigenesis: a new case series and literature review for variant interpretation and pathogenicity. Mol Genet Genomic Med. 2017 Mar 2;5(3):237-250. Denes J et al. Heterogeneous genetic background of the association of pheochromocytoma/paraganglioma and pituitary adenoma: results from a large patient cohort. J Clin Endocrinol Metab. 2015 Mar;100(3):E531-41. Else T et al. Adrenocortical carcinoma and succinate dehydrogenase gene mutations: an observational case series. Eur J Endocrinol. 2017 Nov;177(5):439-444. Korpershoek E et al. SDHA immunohistochemistry detects germline SDHA gene mutations in apparently sporadic paragangliomas and pheochromocytomas. J Clin Endocrinol Metab. 2011 Sep;96(9):E1472-6. Lussey-Lepoutre C et al. In Vivo Detection of Succinate by Magnetic Resonance Spectroscopy as a Hallmark of SDHx Mutations in Paraganglioma. Clin Cancer Res. 2016 Mar 1;22(5):1120-9. Niemeijer ND et al. Succinate Dehydrogenase (SDH)-Deficient Pancreatic Neuroendocrine Tumor Expands the SDH-Related Tumor Spectrum. J Clin Endocrinol Metab. 2015 Oct;100(10):E1386-93. Oudijk L et al. SDHA mutations in adult and pediatric wild-type gastrointestinal stromal tumors. Mod Pathol. 2013 Mar;26(3):456-63. Pantaleo MA et al. SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. J Natl Cancer Inst. 2011 Jun 22;103(12):983-7. Rattenberry E et al. A comprehensive next generation sequencing-based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma. J Clin Endocrinol Metab. 2013 Jul;98(7):E1248-56. Renkema GH et al. SDHA mutations causing a multisystem mitochondrial disease: novel mutations and genetic overlap with hereditary tumors. Eur J Hum Genet. 2015 Feb;23(2):202-9. Wagner AJ et al. Loss of expression of SDHA predicts SDHA mutations in gastrointestinal stromal tumors. Mod Pathol. 2013 Feb;26(2):289-94. (less)
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Pathogenic
(Oct 15, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002020042.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Paragangliomas 5
Mitochondrial complex II deficiency, nuclear type 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV000288157.11
First in ClinVar: Jul 01, 2016 Last updated: Feb 28, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg31*) in the SDHA gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Arg31*) in the SDHA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SDHA are known to be pathogenic (PMID: 22974104, 24781757). This variant is present in population databases (rs142441643, gnomAD 0.04%). This premature translational stop signal has been observed in individual(s) with gastrointestinal stromal tumors (GIST), paragangliomas (PGL), pheochromocytomas (PCC), Carney triad and autosomal-recessive complex II deficiency (PMID: 21505157, 21752896, 22955521, 23174939, 23666964, 24781757, 25494863, 26173966, 26259135). ClinVar contains an entry for this variant (Variation ID: 142601). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jan 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001250478.20
First in ClinVar: May 12, 2020 Last updated: Apr 15, 2024 |
Comment:
SDHA: PVS1, PP1:Strong, PS3:Supporting
Number of individuals with the variant: 12
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Likely pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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Carney triad
Affected status: yes
Allele origin:
germline
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Section on Endocrinology and Genetics, National Institutes of Health / The Eunice Kennedy Shriver National Institute of Child Health and Human Development
Study: Carney Triad
Accession: SCV000222637.1 First in ClinVar: May 01, 2015 Last updated: May 01, 2015 |
Clinical Features:
Stomach GIST (present) , Pulmonary chondroma (present)
Method: Sanger sequence
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800132.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807733.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743955.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001979558.1 First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
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Pathogenic
(Aug 04, 2022)
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no assertion criteria provided
Method: clinical testing
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Mitochondrial complex II deficiency, nuclear type 1
Affected status: yes
Allele origin:
maternal
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Undiagnosed Diseases Network, NIH
Study: Undiagnosed Diseases Network (NIH), UDN
Accession: SCV002818549.1 First in ClinVar: Jan 15, 2023 Last updated: Jan 15, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Weak cry (present) , Meconium stained amniotic fluid (present) , Tall stature (present) , Microcephaly (present) , Macrocephaly (present) , Macrotia (present) , Esotropia (present) … (more)
Weak cry (present) , Meconium stained amniotic fluid (present) , Tall stature (present) , Microcephaly (present) , Macrocephaly (present) , Macrotia (present) , Esotropia (present) , Horizontal nystagmus (present) , Motor stereotypies (present) , Delayed speech and language development (present) , Abnormality of the vertebral column (present) , Abnormal diaphysis morphology (present) , Large hands (present) , Seizure (present) , Intellectual disability, mild (present) , Generalized hypotonia (present) , Abnormal cerebellum morphology (present) , Dystonic disorder (present) , Tremor (present) , Obesity (present) , Pes planus (present) , Long foot (present) , Gait ataxia (present) , Delayed gross motor development (present) , Clumsiness (present) , Positive Romberg sign (present) , Generalized joint hypermobility (present) , Bowing of the legs (present) , Abnormal EKG (present) , Increased body weight (present) , Accelerated skeletal maturation (present) , Cortical thickening of long bone diaphyses (present) , Cerebellar vermis atrophy (present) , Mild conductive hearing impairment (present) , Impaired visuospatial constructive cognition (present) , Absent cupid's bow (present) , Delayed fine motor development (present) , Speech apraxia (present) , Partial beta-EEG (present) , Long palm (present) , Mild receptive language delay (present) , Reduced brain N-acetyl aspartate level by MRS (present) , Cutaneous syndactyly (present) , Short palpebral fissure (present) , Freckled genitalia (present) , Lip pit (present) (less)
Age: 10-19 years
Sex: male
Tissue: Blood
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Pathogenic
(Oct 17, 2023)
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no assertion criteria provided
Method: literature only
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PHEOCHROMOCYTOMA/PARAGANGLIOMA SYNDROME 5
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000246126.3
First in ClinVar: Sep 29, 2015 Last updated: Oct 21, 2023 |
Comment on evidence:
In 4 Dutch patients with paragangliomas (PPGL5; 614165), Korpershoek et al. (2011) identified a heterozygous germline c.91C-T transition (c.91C-T, NM_004168) in the SDHA gene, resulting … (more)
In 4 Dutch patients with paragangliomas (PPGL5; 614165), Korpershoek et al. (2011) identified a heterozygous germline c.91C-T transition (c.91C-T, NM_004168) in the SDHA gene, resulting in an arg31-to-ter (R31X) substitution. The mutation was found in 2 (0.3%) of 692 Dutch controls. All corresponding tumors showed loss of heterozygosity for SDHA and lack of SDHA and SDHB (185470) immunostaining. (less)
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Pathogenic
(Sep 01, 2020)
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no assertion criteria provided
Method: provider interpretation
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Rhabdomyosarcoma
Affected status: yes
Allele origin:
germline
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Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
Accession: SCV001434379.1
First in ClinVar: Oct 03, 2020 Last updated: Oct 03, 2020 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001967500.1 First in ClinVar: Oct 08, 2021 Last updated: Oct 08, 2021 |
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not provided
(-)
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no classification provided
Method: phenotyping only
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Paragangliomas 5
Mitochondrial complex II deficiency, nuclear type 1
Affected status: unknown
Allele origin:
unknown
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GenomeConnect - Invitae Patient Insights Network
Accession: SCV001749411.1
First in ClinVar: Jul 18, 2021 Last updated: Jul 18, 2021 |
Comment:
Variant interpreted as Pathogenic and reported on 04-20-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report … (more)
Variant interpreted as Pathogenic and reported on 04-20-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. (less)
Clinical Features:
Lobular breast carcinoma in situ (present)
Indication for testing: Diagnostic
Age: 60-69 years
Sex: female
Testing laboratory: Invitae
Date variant was reported to submitter: 2020-04-20
Testing laboratory interpretation: Pathogenic
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Frequency of pathogenic germline variants in cancer susceptibility genes in 1336 renal cell carcinoma cases. | Yngvadottir B | Human molecular genetics | 2022 | PMID: 35441217 |
SDHA Germline Variants in Adult Patients With SDHA-Mutant Gastrointestinal Stromal Tumor. | Pantaleo MA | Frontiers in oncology | 2022 | PMID: 35059314 |
Progressive cerebellar atrophy in a patient with complex II and III deficiency and a novel deleterious variant in SDHA: A Counseling Conundrum. | Sturrock BRH | Molecular genetics & genomic medicine | 2021 | PMID: 33960148 |
Prevalence of germline pathogenic variants in 22 cancer susceptibility genes in Swedish pediatric cancer patients. | von Stedingk K | Scientific reports | 2021 | PMID: 33674644 |
Germline Cancer Predisposition Variants in Pediatric Rhabdomyosarcoma: A Report From the Children's Oncology Group. | Li H | Journal of the National Cancer Institute | 2021 | PMID: 33372952 |
Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients. | Aoude LG | Scientific reports | 2020 | PMID: 33077847 |
Prevalence of pathogenic variants in DNA damage response and repair genes in patients undergoing cancer risk assessment and reporting a personal history of early-onset renal cancer. | Hartman TR | Scientific reports | 2020 | PMID: 32782288 |
Whole-genome sequencing of patients with rare diseases in a national health system. | Turro E | Nature | 2020 | PMID: 32581362 |
Exome sequencing in infants with congenital hearing impairment: a population-based cohort study. | Downie L | European journal of human genetics : EJHG | 2020 | PMID: 31827275 |
Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. | Capalbo A | PLoS genetics | 2019 | PMID: 31589614 |
First-positive surveillance screening in an asymptomatic SDHA germline mutation carrier. | White G | Endocrinology, diabetes & metabolism case reports | 2019 | PMID: 31368675 |
Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma. | Ben Aim L | Journal of medical genetics | 2019 | PMID: 30877234 |
Germline SDHA mutations in children and adults with cancer. | Dubard Gault M | Cold Spring Harbor molecular case studies | 2018 | PMID: 30068732 |
Prevalence of Germline Mutations in Cancer Susceptibility Genes in Patients With Advanced Renal Cell Carcinoma. | Carlo MI | JAMA oncology | 2018 | PMID: 29978187 |
Pathogenicity and Penetrance of Germline SDHA Variants in Pheochromocytoma and Paraganglioma (PPGL). | Maniam P | Journal of the Endocrine Society | 2018 | PMID: 29978154 |
SDH-deficient renal cell carcinoma associated with biallelic mutation in succinate dehydrogenase A: comprehensive genetic profiling and its relation to therapy response. | McEvoy CR | NPJ precision oncology | 2018 | PMID: 29872718 |
Pathogenic Germline Variants in 10,389 Adult Cancers. | Huang KL | Cell | 2018 | PMID: 29625052 |
Clinical Aspects of SDHA-Related Pheochromocytoma and Paraganglioma: A Nationwide Study. | van der Tuin K | The Journal of clinical endocrinology and metabolism | 2018 | PMID: 29177515 |
Adrenocortical carcinoma and succinate dehydrogenase gene mutations: an observational case series. | Else T | European journal of endocrinology | 2017 | PMID: 28819017 |
SDHA mutated paragangliomas may be at high risk of metastasis. | Tufton N | Endocrine-related cancer | 2017 | PMID: 28500238 |
Clinical Characterization of the Pheochromocytoma and Paraganglioma Susceptibility Genes SDHA, TMEM127, MAX, and SDHAF2 for Gene-Informed Prevention. | Bausch B | JAMA oncology | 2017 | PMID: 28384794 |
Successful response to pegylated interferon alpha in a patient with recurrent paraganglioma. | Bahougne T | Endocrine-related cancer | 2017 | PMID: 27895137 |
In Vivo Detection of Succinate by Magnetic Resonance Spectroscopy as a Hallmark of SDHx Mutations in Paraganglioma. | Lussey-Lepoutre C | Clinical cancer research : an official journal of the American Association for Cancer Research | 2016 | PMID: 26490314 |
Carney triad can be (rarely) associated with germline succinate dehydrogenase defects. | Boikos SA | European journal of human genetics : EJHG | 2016 | PMID: 26173966 |
Patterns and functional implications of rare germline variants across 12 cancer types. | Lu C | Nature communications | 2015 | PMID: 26689913 |
Recommendations for somatic and germline genetic testing of single pheochromocytoma and paraganglioma based on findings from a series of 329 patients. | Currás-Freixes M | Journal of medical genetics | 2015 | PMID: 26269449 |
Succinate Dehydrogenase (SDH)-Deficient Pancreatic Neuroendocrine Tumor Expands the SDH-Related Tumor Spectrum. | Niemeijer ND | The Journal of clinical endocrinology and metabolism | 2015 | PMID: 26259135 |
15 YEARS OF PARAGANGLIOMA: The association of pituitary adenomas and phaeochromocytomas or paragangliomas. | O'Toole SM | Endocrine-related cancer | 2015 | PMID: 26113600 |
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. | Xiong HY | Science (New York, N.Y.) | 2015 | PMID: 25525159 |
Heterogeneous genetic background of the association of pheochromocytoma/paraganglioma and pituitary adenoma: results from a large patient cohort. | Dénes J | The Journal of clinical endocrinology and metabolism | 2015 | PMID: 25494863 |
SDHA mutations causing a multisystem mitochondrial disease: novel mutations and genetic overlap with hereditary tumors. | Renkema GH | European journal of human genetics : EJHG | 2015 | PMID: 24781757 |
Analysis of all subunits, SDHA, SDHB, SDHC, SDHD, of the succinate dehydrogenase complex in KIT/PDGFRA wild-type GIST. | Pantaleo MA | European journal of human genetics : EJHG | 2014 | PMID: 23612575 |
Succinate dehydrogenase deficiency in pediatric and adult gastrointestinal stromal tumors. | Belinsky MG | Frontiers in oncology | 2013 | PMID: 23730622 |
A comprehensive next generation sequencing-based genetic testing strategy to improve diagnosis of inherited pheochromocytoma and paraganglioma. | Rattenberry E | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23666964 |
Expression of IGF-1 receptor in KIT/PDGF receptor-α wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction. | Nannini M | Future oncology (London, England) | 2013 | PMID: 23252569 |
SDHA mutations in adult and pediatric wild-type gastrointestinal stromal tumors. | Oudijk L | Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc | 2013 | PMID: 23174939 |
Loss of expression of SDHA predicts SDHA mutations in gastrointestinal stromal tumors. | Wagner AJ | Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc | 2013 | PMID: 22955521 |
SDHA loss of function mutations in a subset of young adult wild-type gastrointestinal stromal tumors. | Italiano A | BMC cancer | 2012 | PMID: 22974104 |
SDHA immunohistochemistry detects germline SDHA gene mutations in apparently sporadic paragangliomas and pheochromocytomas. | Korpershoek E | The Journal of clinical endocrinology and metabolism | 2011 | PMID: 21752896 |
SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing. | Pantaleo MA | Journal of the National Cancer Institute | 2011 | PMID: 21505157 |
SDHA is a tumor suppressor gene causing paraganglioma. | Burnichon N | Human molecular genetics | 2010 | PMID: 20484225 |
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Text-mined citations for rs142441643 ...
HelpRecord last updated Apr 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.