ClinVar Genomic variation as it relates to human health
NM_000500.7(CYP21A2):c.955C>T (p.Gln319Ter)
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_000500.7(CYP21A2):c.955C>T (p.Gln319Ter)
Variation ID: 12169 Accession: VCV000012169.43
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6p21.33 6: 32040421 (GRCh38) [ NCBI UCSC ] 6: 32008198 (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 Apr 4, 2013 Oct 8, 2024 Mar 17, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000500.9:c.955C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000491.4:p.Gln319Ter nonsense NM_001128590.4:c.865C>T NP_001122062.3:p.Gln289Ter nonsense NM_001368143.2:c.550C>T NP_001355072.1:p.Gln184Ter nonsense NM_001368144.2:c.550C>T NP_001355073.1:p.Gln184Ter nonsense NC_000006.12:g.32040421C>T NC_000006.11:g.32008198C>T NG_007941.3:g.7117C>T NG_008337.2:g.73954G>A NG_045215.1:g.2650C>T LRG_829:g.7117C>T LRG_829t1:c.955C>T LRG_829p1:p.Gln319Ter - Protein change
- Q319*, Q289*, Q184*
- Other names
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Q318*
- Canonical SPDI
- NC_000006.12:32040420: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.
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The Genome Aggregation Database (gnomAD) 0.00339
1000 Genomes Project 30x 0.03170
- Links
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
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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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CYP21A2 | - | - |
GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh37 |
23 | 354 | |
LOC106780800 | - | - | - |
GRCh38 GRCh38 |
- | 304 |
TNXB | - | - |
GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh38 GRCh37 |
2348 | 2540 |
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 (13) |
criteria provided, multiple submitters, no conflicts
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Mar 17, 2024 | RCV000012951.28 | |
Pathogenic (10) |
criteria provided, multiple submitters, no conflicts
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Jun 7, 2023 | RCV000711391.22 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 20, 2022 | RCV002222348.1 | |
CYP21A2-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Jul 12, 2024 | RCV003924828.2 |
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
(-)
|
criteria provided, single submitter
Method: clinical testing
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Congenital adrenal hyperplasia, due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
germline
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Centogene AG - the Rare Disease Company
Accession: SCV001424397.1
First in ClinVar: Jul 27, 2020 Last updated: Jul 27, 2020 |
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Pathogenic
(Dec 19, 2019)
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criteria provided, single submitter
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
unknown
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Baylor Genetics
Accession: SCV001524847.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].
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Pathogenic
(Mar 05, 2022)
|
criteria provided, single submitter
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
germline
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DASA
Accession: SCV002107127.2
First in ClinVar: Mar 28, 2022 Last updated: Apr 02, 2022 |
Comment:
The c.955C>T;p.(Gln319*) variant creates a premature translational stop signal in the CYP21A2 gene. It is expected to result in an absent or disrupted protein product … (more)
The c.955C>T;p.(Gln319*) variant creates a premature translational stop signal in the CYP21A2 gene. It is expected to result in an absent or disrupted protein product - PVS1. Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 3267225) - PS3. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar: 12169; PMID: 20301350; PMID: 3267225; PMID: 12220458; PMID: 29715434; PMID: 28819757; PMID: 12220458; PMID: 28392195) - PS4. The p.(Gln319*) was detected in trans with a pathogenic variant (PMID: 26804566) - PM3. In summary, the currently available evidence indicates that the variant is pathogenic. (less)
Number of individuals with the variant: 2
Sex: mixed
Geographic origin: Brazil
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Pathogenic
(Nov 03, 2022)
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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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003332125.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
This sequence change creates a premature translational stop signal (p.Gln319*) in the CYP21A2 gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Gln319*) in the CYP21A2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CYP21A2 are known to be pathogenic (PMID: 10857554). The frequency data for this variant in the population databases (gnomAD) is considered unreliable due to the presence of homologous sequence, such as pseudogenes or paralogs, in the genome. This premature translational stop signal has been observed in individual(s) with classic salt-wasting, simple virilizing, and non-classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency (PMID: 3267225, 23359698, 25538881, 26804566, 30995443). This variant is also known as p.Q318X. ClinVar contains an entry for this variant (Variation ID: 12169). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
|
Neuberg Centre For Genomic Medicine, NCGM
Accession: SCV004048452.1
First in ClinVar: Oct 28, 2023 Last updated: Oct 28, 2023 |
Comment:
The c.955C>T (p.Gln319Ter) stop gained variant in CYP21A2 gene has been reported previously in patients affected with adrenal hyperplasia (Doleschall M. et al., 2017). The … (more)
The c.955C>T (p.Gln319Ter) stop gained variant in CYP21A2 gene has been reported previously in patients affected with adrenal hyperplasia (Doleschall M. et al., 2017). The p.Gln319Ter variant is reported with the allele frequency (0.01%) in the gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The nucleotide change in CYP21A2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. (less)
Clinical Features:
Clitoral hypertrophy (present) , Hypogonadism (present) , Abnormal circulating antimullerian hormone concentration (present) , Increased serum testosterone level (present)
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Pathogenic
(Jun 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001469966.3
First in ClinVar: Jan 26, 2021 Last updated: Jan 06, 2024 |
Comment:
The CYP21A2 c.955C>T (p.Gln319*) variant (also known as Q319X or Q318X) causes the premature termination of CYP21A2 protein synthesis. In the published literature, this variant … (more)
The CYP21A2 c.955C>T (p.Gln319*) variant (also known as Q319X or Q318X) causes the premature termination of CYP21A2 protein synthesis. In the published literature, this variant has been reported as usually being associated with a salt-wasting CAH phenotype (PMIDs: 30995443 (2019), 30048636 (2018), 26804566 (2016), 23269230 (2013), 15858147 (2005), 8034294 (1994), 3267225 (1988)). The frequency of this variant in the general population, 0.00027 (9/33386 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. (less)
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Pathogenic
(Mar 17, 2024)
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criteria provided, single submitter
Method: research
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: unknown
Allele origin:
germline
|
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004804833.2
First in ClinVar: Mar 30, 2024 Last updated: Apr 06, 2024 |
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Pathogenic
(Aug 03, 2017)
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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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Eurofins Ntd Llc (ga)
Accession: SCV000330930.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 7
Sex: mixed
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Pathogenic
(Dec 17, 2019)
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criteria provided, single submitter
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV001193783.2
First in ClinVar: Apr 06, 2020 Last updated: Jul 06, 2020 |
Comment:
NM_000500.7(CYP21A2):c.955C>T(Q319*) is classified as pathogenic in the context of congenital adrenal hyperplasia, CYP21A2-related and is associated with the classic form of the disease. Sources cited … (more)
NM_000500.7(CYP21A2):c.955C>T(Q319*) is classified as pathogenic in the context of congenital adrenal hyperplasia, CYP21A2-related and is associated with the classic form of the disease. Sources cited for classification include the following: PMID 14715874, 3267225, 23359698 and 23769969. Classification of NM_000500.7(CYP21A2):c.955C>T(Q319*) is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. (less)
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Pathogenic
(Nov 24, 2015)
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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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Clinical Genetics and Genomics, Karolinska University Hospital
Accession: SCV001449835.1
First in ClinVar: Dec 12, 2020 Last updated: Dec 12, 2020 |
Number of individuals with the variant: 20
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Pathogenic
(Feb 11, 2020)
|
criteria provided, single submitter
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
germline
|
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital
Accession: SCV001984016.1
First in ClinVar: Oct 30, 2021 Last updated: Oct 30, 2021 |
|
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Pathogenic
(Mar 20, 2022)
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criteria provided, single submitter
Method: clinical testing
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Congenital adrenal hyperplasia
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002500529.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
Comment:
Variant summary: CYP21A2 c.955C>T (p.Gln319X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Variant summary: CYP21A2 c.955C>T (p.Gln319X) 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. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 0.0001 in 249104 control chromosomes. c.955C>T has been widely reported in the literature in multiple individuals affected with Congenital Adrenal Hyperplasia (example, Elmougy_2021, New_2013). These data indicate that the variant is very likely to be associated with disease. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Mar 24, 2022)
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criteria provided, single submitter
Method: clinical testing
|
Not provided
Affected status: yes
Allele origin:
germline
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AiLife Diagnostics, AiLife Diagnostics
Accession: SCV002502921.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
Number of individuals with the variant: 1
Secondary finding: no
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Pathogenic
(May 22, 2022)
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criteria provided, single submitter
Method: clinical testing
|
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
germline
|
3billion
Accession: SCV002521233.1
First in ClinVar: Jun 03, 2022 Last updated: Jun 03, 2022 |
Comment:
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.036%). Stop-gained (nonsense): predicted to result in a … (more)
The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.036%). Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000012169 / PMID: 3267225 ). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Hyponatremia (present) , Hyperkalemia (present) , Ambiguous genitalia (present) , Vomiting (present) , Elevated circulating 17-hydroxyprogesterone concentration (present)
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Pathogenic
(Jun 07, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Athena Diagnostics
Accession: SCV000841754.4
First in ClinVar: Oct 20, 2018 Last updated: Jan 26, 2024 |
Comment:
This variant is expected to result in the loss of a functional protein. Frequency data for this variant in the general population cannot be distinguished … (more)
This variant is expected to result in the loss of a functional protein. Frequency data for this variant in the general population cannot be distinguished from that of the CYP21P pseudogene, and are therefore uninformative in assessment of variant pathogenicity (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant is also referred to by codon 318 in published literature. This variant has been identified in at least one individual with clinical features associated with this gene. In multiple individuals, this variant has been seen in trans with other recessive pathogenic variants in CYP21A2, suggesting this variant is also pathogenic. Assessment of experimental evidence suggests this variant results in abnormal protein function. Variant caused a marked decrease in 21-hydroxylase mRNA levels (PMID: 3267225). (less)
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Pathogenic
(Mar 02, 2023)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Revvity Omics, Revvity
Accession: SCV002018107.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
|
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Pathogenic
(Jul 16, 2023)
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criteria provided, single submitter
Method: clinical testing
|
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
(Autosomal recessive inheritance)
Affected status: no
Allele origin:
germline
|
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002557086.2
First in ClinVar: Aug 04, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with congenital adrenal hyperplasia due to 21-hydroxylase deficiency (MIM#201910) and hyperandrogenism nonclassic type due to 21-hydroxylase deficiency (MIM#201910). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous (according to Fulgent Genetics report). (I) 0304 - Variant is present in gnomAD (v3) <0.01 for a recessive condition (523 heterozygotes, 0 homozygotes). (SP) 0701 - Other variants predicted to result in NMD comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER). (SP) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It has been reported as one of the most frequent disease-causing CYP21A2 variants. (ClinVar, PMIDs: 31586465, 32616876) (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
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Pathogenic
(Aug 18, 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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Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005197684.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
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Pathogenic
(Aug 01, 2002)
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no assertion criteria provided
Method: literature only
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ADRENAL HYPERPLASIA, CONGENITAL, DUE TO 21-HYDROXYLASE DEFICIENCY, SALT-WASTING TYPE
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000033195.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
Globerman et al. (1988) identified a T-to-C substitution at nucleotide 1994 in exon 8 of the CYP21A2 gene, resulting in a stop codon at position … (more)
Globerman et al. (1988) identified a T-to-C substitution at nucleotide 1994 in exon 8 of the CYP21A2 gene, resulting in a stop codon at position 318 (Q318X). Individuals homozygous for this mutation have the salt-wasting form of 21-hydroxylase deficiency (201910) and no enzymatic activity. This mutation is normally present in the CYP21 pseudogene. In a Spanish population, Ezquieta et al. (2002) provided data on the contributions of gene conversion and founder effect to the distribution of the 2 most frequent severe point mutations of the CYP21A2 gene causing congenital adrenal hyperplasia: the 655G splicing mutation at intron 2 (613815.0006) and gln318-to-ter. Both mechanisms were found to contribute to the mutant alleles in different degrees. The 655G splicing mutation (accounting for 15.5% of alleles) seemed to be almost exclusively related to recent conversion events, whereas Q318X (accounting for 8.3% of alleles) was more likely to be due to the dissemination of remotely generated mutant alleles. (less)
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Pathogenic
(Apr 27, 2018)
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no assertion criteria provided
Method: clinical testing
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: yes
Allele origin:
germline
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Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City
Accession: SCV000854658.1
First in ClinVar: Jan 06, 2018 Last updated: Jan 06, 2018 |
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Pathogenic
(Jul 12, 2024)
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no assertion criteria provided
Method: clinical testing
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CYP21A2-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004746566.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The CYP21A2 c.955C>T variant is predicted to result in premature protein termination (p.Gln319*). This is a common deleterious variant that likely originated from the pseudogene … (more)
The CYP21A2 c.955C>T variant is predicted to result in premature protein termination (p.Gln319*). This is a common deleterious variant that likely originated from the pseudogene CYP21A1P via gene conversion. As a nonsense variant resulting in a null allele, this variant is associated with salt-wasting (SW) congenital adrenal hyperplasia (CAH) (also known as Q318X; see for example at New et al. 2013. PubMed ID: 23359698; Finkielstain et al. 2011. PubMed ID: 20926536). This variant is interpreted as pathogenic. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
|
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Lifecell International Pvt. Ltd
Accession: SCV001482473.2
First in ClinVar: Mar 07, 2021 Last updated: Mar 07, 2021 |
Comment:
The variant in exon 8 of the CYP21A2 gene c.955C>T;p.Gln319Ter (NM_000500.7) also know as Q318*. This variant was observed in a proband with an increased … (more)
The variant in exon 8 of the CYP21A2 gene c.955C>T;p.Gln319Ter (NM_000500.7) also know as Q318*. This variant was observed in a proband with an increased level of 17-OHP enzyme (>287.3 nmol/L) which was screened for advanced newborn screening with confirmatory genetic reflex testing at lifecell diagnostics. The reference base is conserved across the species and in-silico predictions by Polyphen and SIFT are damaging. The observed variant has a minor allele frequency of 0.4% in gnomAD database and not reported in 1000 genome database.The reference base is conserved across the species and in-silico predictions by CADD is deleterious. The gene CYP21A2 has a low rate of benign loss of function variants as indicated by a high LoF variants Z-Score of 2.86. The p.Gln319Ter variant is a loss of function variant in the gene CYP21A2, which is intolerant of Loss of Function variants, as indicated by the presence of existing pathogenic loss of function variant NP_000491.4:p.Trp20Ter and 4 others. There is another pathogenic loss of function variant 165 residues downstream of the variant p.Gln319Ter.This variant has previously been reported for adrenal hyperplasia by Doleschall M et al.,2017-PMID: 28401898; Concolino P. et al., 2020-PMID: 32185686; Kharrat M et al., 2004- PMID: 21532487 and Globerman H et al., 1988-PMID: 3267225). (less)
Indication for testing: Decreased level of 17-OHP enzyme (>287.3 nmol/L)
Ethnicity/Population group: Asian
Geographic origin: India
Testing laboratory: GTRL000507720
Testing laboratory interpretation: Pathogenic
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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: SCV001800361.1 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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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: SCV001952694.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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not provided
(-)
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no classification provided
Method: literature only
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Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Affected status: not provided
Allele origin:
unknown
|
GeneReviews
Accession: SCV000086806.2
First in ClinVar: Oct 01, 2013 Last updated: Oct 01, 2022 |
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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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Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients. | Mao W | PeerJ | 2021 | PMID: 34540367 |
A novel 9 bp deletion (c.1271_1279delGTGCCCGCG) in exon 10 of CYP21A2 gene causing severe congenital adrenal hyperplasia. | Anastasovska V | Endocrine | 2021 | PMID: 33715135 |
Molecular Analysis of 21-Hydroxylase Deficiency Reveals Two Novel Severe Genotypes in Affected Newborns. | Concolino P | Molecular diagnosis & therapy | 2021 | PMID: 33710594 |
Genetic profiling of CAH Egyptian children: rapid guide to clinical interpretation of common mutations. | Elmougy F | Journal of endocrinological investigation | 2021 | PMID: 32358738 |
Application of Next-Generation Sequencing for Genetic Diagnosis in Neonatal Intensive Care Units: Results of a Multicenter Study in China. | Zhu T | Frontiers in genetics | 2020 | PMID: 33240318 |
Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility. | Cheema H | NPJ genomic medicine | 2020 | PMID: 33083013 |
Primary Adrenocortical Insufficiency Case Series in the Neonatal Period: Genetic Etiologies Are More Common Than Expected. | Gao J | Frontiers in pediatrics | 2020 | PMID: 32903448 |
p.Gln318X and p.Val281Leu as the Major Variants of CYP21A2 Gene in Children with Idiopathic Premature Pubarche. | Soveizi M | International journal of endocrinology | 2020 | PMID: 32714392 |
Genotype-phenotype correlations in children and adolescents with nonclassical congenital adrenal hyperplasia due to 21-hydroxylase deficiency. | Dörr HG | Molecular and cellular pediatrics | 2020 | PMID: 32647925 |
EMQN best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency. | Baumgartner-Parzer S | European journal of human genetics : EJHG | 2020 | PMID: 32616876 |
An exome-first approach to aid in the diagnosis of primary ciliary dyskinesia. | Shamseldin HE | Human genetics | 2020 | PMID: 32367404 |
Simple virilising congenital adrenal hyperplasia in monozygotic twins: A rare report and review of previous cases. | Muthuvel B | Pediatric endocrinology, diabetes, and metabolism | 2020 | PMID: 32272826 |
A rare CYP21A2 haplotype clarifies the phenotype-genotype discrepancy in an Italian patient with Non Classical Congenital Adrenal Hyperplasia (NC-CAH). | Concolino P | Molecular biology reports | 2020 | PMID: 32185686 |
Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging. | Hou YC | Proceedings of the National Academy of Sciences of the United States of America | 2020 | PMID: 31980526 |
21-Hydroxylase deficiency: Mutational spectrum and Genotype-Phenotype relations analyses by next-generation sequencing and multiplex ligation-dependent probe amplification. | Turan I | European journal of medical genetics | 2020 | PMID: 31586465 |
Detection of a novel severe mutation affecting the CYP21A2 gene in a Chilean male with salt wasting congenital adrenal hyperplasia. | Arteaga E | Endocrine | 2020 | PMID: 31571129 |
Implementation of a Targeted Next-Generation Sequencing Panel for Constitutional Newborn Screening in High-Risk Neonates. | Lee H | Yonsei medical journal | 2019 | PMID: 31637888 |
Analysis of phenotypes and genotypes in 84 patients with 21-Hydroxylase deficiency in southern China. | Hou L | Steroids | 2019 | PMID: 31446012 |
[Clinical features and genetic characteristics of 33 patients with simple virilizing form of 21-hydroxylase deficiency]. | Zeng LT | Zhonghua nei ke za zhi | 2019 | PMID: 31159521 |
Identification of novel and rare CYP21A2 variants in Chinese patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency. | Xu J | Clinical biochemistry | 2019 | PMID: 30995443 |
CYP21A2 Gene Pathogenic Variants: A Multicenter Study on Genotype-Phenotype Correlation from a Portuguese Pediatric Cohort. | Santos-Silva R | Hormone research in paediatrics | 2019 | PMID: 30889569 |
Identification of the Germline Mutation Profile in Esophageal Squamous Cell Carcinoma by Whole Exome Sequencing. | Deng J | Frontiers in genetics | 2019 | PMID: 30833958 |
Clinical and molecular profile of newborns with confirmed or suspicious congenital adrenal hyperplasia detected after a public screening program implementation. | Kopacek C | Jornal de pediatria | 2019 | PMID: 29715434 |
Clinical presentation and mutational spectrum in a series of 166 patients with classical 21-hydroxylase deficiency from South China. | Su L | Clinica chimica acta; international journal of clinical chemistry | 2018 | PMID: 30048636 |
Modeling Congenital Adrenal Hyperplasia and Testing Interventions for Adrenal Insufficiency Using Donor-Specific Reprogrammed Cells. | Ruiz-Babot G | Cell reports | 2018 | PMID: 29386111 |
A genetic epidemiology study of congenital adrenal hyperplasia in Italy. | Gialluisi A | Clinical genetics | 2018 | PMID: 28644547 |
Clinical characteristics of Taiwanese children with congenital adrenal hyperplasia due to 21-hydroxylase deficiency detected by neonatal screening. | Liu SY | Journal of the Formosan Medical Association = Taiwan yi zhi | 2018 | PMID: 28392195 |
Development of CYP21A2 Genotyping Assay for the Diagnosis of Congenital Adrenal Hyperplasia. | Prado MJ | Molecular diagnosis & therapy | 2017 | PMID: 28819757 |
A unique haplotype of RCCX copy number variation: from the clinics of congenital adrenal hyperplasia to evolutionary genetics. | Doleschall M | European journal of human genetics : EJHG | 2017 | PMID: 28401898 |
21-hydroxylase deficiency-induced congenital adrenal hyperplasia in 230 Chinese patients: Genotype-phenotype correlation and identification of nine novel mutations. | Wang R | Steroids | 2016 | PMID: 26804566 |
CYP21A2 genetics: When genotype does not fit phenotype. | Sani I | Clinical biochemistry | 2016 | PMID: 26209023 |
21-Hydroxylase-Deficient Congenital Adrenal Hyperplasia. | Adam MP | - | 2016 | PMID: 20301350 |
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 |
Genetic defects of the CYP21A2 gene in girls with premature adrenarche. | Skordis N | Journal of endocrinological investigation | 2015 | PMID: 25481255 |
Phenotypic variability of hyperandrogenemia in females heterozygous for CYP21A2 mutations. | Neocleous V | Indian journal of endocrinology and metabolism | 2014 | PMID: 25538881 |
A case with combined rare inborn metabolic disorders: congenital adrenal hyperplasia and ornithine transcarbamylase deficiency. | Kim YM | Gene | 2013 | PMID: 23769969 |
Genotype-phenotype correlation in 1,507 families with congenital adrenal hyperplasia owing to 21-hydroxylase deficiency. | New MI | Proceedings of the National Academy of Sciences of the United States of America | 2013 | PMID: 23359698 |
Erroneous prenatal diagnosis of congenital adrenal hyperplasia owing to a duplication of the CYP21A2 gene. | Lekarev O | Journal of perinatology : official journal of the California Perinatal Association | 2013 | PMID: 23269230 |
Detection of a frequent duplicated CYP21A2 gene carrying a Q318X mutation in a general population with quantitative PCR methods. | Kharrat M | Diagnostic molecular pathology : the American journal of surgical pathology, part B | 2011 | PMID: 21532487 |
Duplications of the functional CYP21A2 gene are primarily restricted to Q318X alleles: evidence for a founder effect. | Kleinle S | The Journal of clinical endocrinology and metabolism | 2009 | PMID: 19773403 |
Predisposition for de novo gene aberrations in the offspring of mothers with a duplicated CYP21A2 gene. | Baumgartner-Parzer SM | The Journal of clinical endocrinology and metabolism | 2007 | PMID: 17164306 |
Validation and clinical application of a locus-specific polymerase chain reaction- and minisequencing-based assay for congenital adrenal hyperplasia (21-hydroxylase deficiency). | Keen-Kim D | The Journal of molecular diagnostics : JMD | 2005 | PMID: 15858147 |
Molecular genetic analysis of Tunisian patients with a classic form of 21-hydroxylase deficiency: identification of four novel mutations and high prevalence of Q318X mutation. | Kharrat M | The Journal of clinical endocrinology and metabolism | 2004 | PMID: 14715874 |
Duplication of the CYP21A2 gene complicates mutation analysis of steroid 21-hydroxylase deficiency: characteristics of three unusual haplotypes. | Koppens PF | Human genetics | 2002 | PMID: 12384784 |
Gene conversion (655G splicing mutation) and the founder effect (Gln318Stop) contribute to the most frequent severe point mutations in congenital adrenal hyperplasia (21-hydroxylase deficiency) in the Spanish population. | Ezquieta B | Clinical genetics | 2002 | PMID: 12220458 |
Molecular characterization of mutations in Indian children with congenital adrenal hyperplasia due to steroid 21-hydroxylase deficiency. | Mathur R | Journal of pediatric endocrinology & metabolism : JPEM | 2001 | PMID: 11220701 |
Mutations in the CYP21 B gene in a Chilean population with simple virilizing congenital adrenal hyperplasia. | Fardella CE | Journal of endocrinological investigation | 2000 | PMID: 10908170 |
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency. | White PC | Endocrine reviews | 2000 | PMID: 10857554 |
A rapid screening for steroid 21-hydroxylase mutations in patients with congenital adrenal hyperplasia. Mutations in brief no. 247. Online. | Kapelari K | Human mutation | 1999 | PMID: 10408786 |
Conventional molecular diagnosis of steroid 21-hydroxylase deficiency using mismatched primers and polymerase chain reaction. | Tajima T | Endocrine research | 1997 | PMID: 9378109 |
Who is a carrier? Detection of unsuspected mutations in 21-hydroxylase deficiency. | Witchel SS | American journal of medical genetics | 1996 | PMID: 8741909 |
Characterization of mutations on the rare duplicated C4/CYP21 haplotype in steroid 21-hydroxylase deficiency. | Wedell A | Human genetics | 1994 | PMID: 8034294 |
Nonsense mutation causing steroid 21-hydroxylase deficiency. | Globerman H | The Journal of clinical investigation | 1988 | PMID: 3267225 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP21A2 | - | - | - | - |
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Text-mined citations for rs7755898 ...
HelpRecord last updated Oct 13, 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.