NM_003002.4(SDHD):c.430_435del (p.Tyr144_His145del) AND Hereditary cancer-predisposing syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 11, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002331890.2

Allele description

NM_003002.4(SDHD):c.430_435del (p.Tyr144_His145del)

Gene:

SDHD:succinate dehydrogenase complex subunit D [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.1

Genomic location:

Preferred name:

NM_003002.4(SDHD):c.430_435del (p.Tyr144_His145del)

HGVS:

NC_000011.10:g.112094920_112094925del
NG_012337.3:g.13074_13079del
NM_001276503.2:c.*27_*32del
NM_001276504.2:c.313_318del
NM_001276506.2:c.*128_*133del
NM_003002.4:c.430_435delMANE SELECT
NP_001263433.1:p.Tyr105_His106del
NP_002993.1:p.Tyr144_His145del
LRG_9t1:c.430_435del
LRG_9:g.13074_13079del
LRG_9p1:p.Tyr144_His145del
NC_000011.9:g.111965642_111965647del
NC_000011.9:g.111965644_111965649del
NM_003002.2:c.430_435delTATCAC
NR_077060.2:n.519_524del

Molecular consequence:

NM_001276503.2:c.*27_*32del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276506.2:c.*128_*133del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001276504.2:c.313_318del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003002.4:c.430_435del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_077060.2:n.519_524del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002630885	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Likely pathogenic (Jul 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002630885

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Likely pathogenic
(Jul 11, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genetic and clinical aspects of paediatric pheochromocytomas and paragangliomas.

Petenuci J, Guimaraes AG, Fagundes GFC, Benedetti AFF, Afonso ACF, Pereira MAA, Zerbini MCN, Siqueira S, Yamauchi F, Soares SC, Srougi V, Tanno FY, Chambo JL, Lopes RI, Denes FT, Hoff AO, Latronico AC, Mendonca BB, Fragoso MCBV, Almeida MQ.

Clin Endocrinol (Oxf). 2021 Jul;95(1):117-124. doi: 10.1111/cen.14467. Epub 2021 Mar 28.

PubMed [citation]

PMID:: 33745191

Details of each submission

From Ambry Genetics, SCV002630885.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The c.430_435delTATCAC variant (also known as p.Y144_H145del) is located in coding exon 4 of the SDHD gene. This variant results from an in-frame TATCAC deletion at nucleotide positions 430 to 435. This results in the in-frame deletion of tyrosine and histidine residues at codons 144 and 145. This variant has been detected in individuals with pheochromocytomas and/or paragangliomas diagnosed under age 50 (Petenuci J et al. Clin Endocrinol (Oxf), 2021 07;95:117-124; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). These amino acid positions are well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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