ClinVar Genomic variation as it relates to human health
NM_000500.9(CYP21A2):c.188A>T (p.His63Leu)
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.
Pathogenic(2); Likely pathogenic(1); Benign(2); Likely benign(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000500.9(CYP21A2):c.188A>T (p.His63Leu)
Variation ID: 12183 Accession: VCV000012183.14
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 6p21.33 6: 32038610 (GRCh38) [ NCBI UCSC ] 6: 32006387 (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 Jun 28, 2015 Sep 29, 2024 Oct 1, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000500.9:c.188A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000491.4:p.His63Leu missense NM_001128590.4:c.188A>T NP_001122062.3:p.His63Leu missense NM_001368143.2:c.-237A>T 5 prime UTR NM_001368144.2:c.-147A>T 5 prime UTR NC_000006.12:g.32038610A>T NC_000006.11:g.32006387A>T NG_007941.3:g.5306A>T NG_045215.1:g.839A>T LRG_829:g.5306A>T LRG_829t1:c.188A>T LRG_829p1:p.His63Leu - Protein change
- H63L
- Other names
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H62L
- Canonical SPDI
- NC_000006.12:32038609:A: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) 0.00995
1000 Genomes Project 30x 0.01608
The Genome Aggregation Database (gnomAD), exomes 0.04407
Exome Aggregation Consortium (ExAC) 0.09368
- Links
- Comment on variant
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 |
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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Benign (2) |
criteria provided, single submitter
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May 28, 2019 | RCV000012965.12 | |
Benign (1) |
criteria provided, single submitter
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Feb 23, 2015 | RCV000173141.14 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
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Sep 28, 2022 | RCV002472929.12 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Oct 1, 2022 | RCV002307363.8 |
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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Benign
(Feb 23, 2015)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000224230.5
First in ClinVar: Jun 28, 2015 Last updated: Jun 28, 2015 |
Number of individuals with the variant: 2
Sex: mixed
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Benign
(May 28, 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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Mendelics
Accession: SCV001137076.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Likely pathogenic
(Oct 01, 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: SCV002050902.2
First in ClinVar: Jan 08, 2022 Last updated: Nov 19, 2022 |
Comment:
Variant summary: CYP21A2 c.188A>T (p.His63Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign … (more)
Variant summary: CYP21A2 c.188A>T (p.His63Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant was present at a high frequency in 7520 out of 19,2468 control chromosomes in the gnomAD database, however, the inability of this data to distinguish the occurrence of this variant in the CYP21A1P pseudogene versus the real CYP21A2 gene makes this data unreliable to formulate conclusive opinions. In a cross-sectional review of the literature, c.188A>T has been reported in isolation as a compound heterozygote in trans with other CYP21A2 alleles in individuals affected with non-classic and simple virilizing forms of Congenital Adrenal Hyperplasia (example, Menassa_2008, Taboas_2013, Fernandez_2020, Nagasaki_2009) as well as a complex allele in cis with other putative CYP21A2 alleles (example, Soardi_2008, Liu_2022) and as a non-informative genotype (without a clear second allele specification) (example, Wang_2021, Yoon_2021). At-least one of these studies reports comprehensive genotyping utilizing orthogonal technologies to confirm the allele origin (example, Fernandez_2020). A recent report by the European Molecular Genetics Quality Network (EMQN) describing the best practice guidelines for molecular genetic testing and reporting of 21-hydroxylase deficiency lists this variant among those classified as "definitely pathogenic" for a non-classic phenotype (Baumgartner-Parzer_2020). These data indicate that the variant in isolation is likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in variable levels of CYP21A2 enzyme activity depending upon the substrate utilized, namely 17-Hydroxyprogesterone or Progesterone. The reported activities range from one study reporting 70.8% of WT for conversion of 17OHP to 11-deoxycortisol (i.e., a 29.2% reduction in activity) and 66.5% of WT for conversion of Progesterone to 11-Deoxycorticosterone (DOC) (i.e., a 33.5% reduction in activity) with a similar reduction in maximal velocity (Vmax) (72.17% and 69.16% respectively) (Menassa_2008), while another study reporting a more pronounced impact on activity, 44.5% of WT with 17-OHP substrate and 20.7% of WT with Progesterone substrate (Soardi_2008) and a more pronounced impact of maximal velocity (Vmax) (13% and 8.65% respectively). Two 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 benign. Based on the evidence outlined above, the variant was classified as likely pathogenic. (less)
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Pathogenic
(Sep 28, 2022)
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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: SCV004221768.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
The variant has been found in at least one symptomatic individual. Functional evidence suggests that this variant may impact protein function. The variant occurs in … (more)
The variant has been found in at least one symptomatic individual. Functional evidence suggests that this variant may impact protein function. The variant occurs in multiple cases with a lone recessive pathogenic/likely pathogenic variant in the same gene, and have phenotype known to be consistent with disease. Based on the available information, this variant is classified as pathogenic. (less)
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Likely benign
(-)
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criteria provided, single submitter
Method: not provided
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not provided
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Breakthrough Genomics, Breakthrough Genomics
Accession: SCV005225558.1
First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024 |
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Pathogenic
(Sep 28, 2022)
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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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Athena Diagnostics
Accession: SCV002771866.2
First in ClinVar: Dec 31, 2022 Last updated: Jan 26, 2024 |
Comment:
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 … (more)
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. In some published literature, this variant is referred to as c.185A>T (p.His62Leu). This variant has been seen in trans with other recessive pathogenic CYP21A2 variants in multiple individuals with congenital and also nonclassic forms of CAH. Assessment of experimental evidence suggests this variant results in abnormal protein function. See PMID: 18319307, 18381579. (less)
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Pathogenic
(Jun 01, 2008)
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no assertion criteria provided
Method: literature only
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ADRENAL HYPERPLASIA, CONGENITAL, DUE TO 21-HYDROXYLASE DEFICIENCY
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000033209.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 26, 2016 |
Comment on evidence:
Of 60 novel mutations in CYP21 identified in a screen of 2,900 patients with steroid 21-hydroxylase deficiency (201910), Menassa et al. (2008) found that a … (more)
Of 60 novel mutations in CYP21 identified in a screen of 2,900 patients with steroid 21-hydroxylase deficiency (201910), Menassa et al. (2008) found that a his-to-leu substitution at codon 62 (H62L) was the most frequent. The H62L substitution, which arises from an A-to-T transversion at nucleotide 185 in exon 1 of the CYP21 gene, was found in 13 patients from 12 unrelated families, either isolated or associated on the same allele with a mild mutation. In isolation, or when associated with a partial conversion of the promoter, the H62L mutation was responsible for a nonclassic form; associated with the P453S (613815.0010) or P30L (613815.0004) mutations, H62L contributed to a simple virilizing phenotype more severe than that associated with P453S or P30L alone, but not as severe as the phenotype associated with I172N (613815.0001). Analysis of a 3-dimensional model structure of the CYP21 protein localized the H62L mutation to the beta-1-sheet region, in a large hydrophobic area considered important for membrane anchoring. Soardi et al. (2008) found that the H62L mutant protein showed an activity compatible with a nonclassic mutation in functional assays. Determination of apparent kinetic constants revealed that the substrate binding capacity was in the same magnitude for mutant and normal enzyme. Soardi et al. (2008) found that the H62L mutation was associated with other mutations in both Brazilian and Scandinavian patients. In the Scandinavian patients H62L was associated on the paternal allele with the nonclassic P453S (613815.0010) mutation. In vitro activity data revealed a synergistic effect of the H62L+P453S mutation, which may explain the mild simple virilizing phenotype in these patients. (less)
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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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Comprehensive Analysis of Congenital Adrenal Hyperplasia Using Long-Read Sequencing. | Liu Y | Clinical chemistry | 2022 | PMID: 35714169 |
Targeted gene panel sequencing for molecular diagnosis of congenital adrenal hyperplasia. | Wang W | The Journal of steroid biochemistry and molecular biology | 2021 | PMID: 33864926 |
Genotype and clinical outcomes in children with congenital adrenal hyperplasia. | Yoon JY | Pediatrics international : official journal of the Japan Pediatric Society | 2021 | PMID: 32965796 |
Outcome of Newborn Screening for Congenital Adrenal Hyperplasia at Two Time Points. | Eshragh N | Hormone research in paediatrics | 2020 | PMID: 32659761 |
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 |
Genetic characterization of a large cohort of Argentine 21-hydroxylase Deficiency. | Fernández CS | Clinical endocrinology | 2020 | PMID: 32289882 |
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 |
Novel variants of CYP21A2 in Vietnamese patients with congenital adrenal hyperplasia. | Chi DV | Molecular genetics & genomic medicine | 2019 | PMID: 30816000 |
Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations. | Bruque CD | Scientific reports | 2016 | PMID: 27966633 |
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 |
Novel method to characterize CYP21A2 in Florida patients with congenital adrenal hyperplasia and commercially available cell lines. | Greene CN | Molecular genetics and metabolism reports | 2014 | PMID: 27896104 |
One hundred years of congenital adrenal hyperplasia in Sweden: a retrospective, population-based cohort study. | Gidlöf S | The lancet. Diabetes & endocrinology | 2013 | PMID: 24622265 |
Both positive and negative selection pressures contribute to the polymorphism pattern of the duplicated human CYP21A2 gene. | Szabó JA | PloS one | 2013 | PMID: 24312389 |
Isolated p.H62L Mutation in the CYP21A2 Gene in a Simple Virilizing 21-Hydroxylase Deficient Patient. | Taboas M | Case reports in genetics | 2013 | PMID: 23936690 |
Genotype-phenotype correlation in 153 adult patients with congenital adrenal hyperplasia due to 21-hydroxylase deficiency: analysis of the United Kingdom Congenital adrenal Hyperplasia Adult Study Executive (CaHASE) cohort. | Krone N | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23337727 |
Carrier testing for severe childhood recessive diseases by next-generation sequencing. | Bell CJ | Science translational medicine | 2011 | PMID: 21228398 |
Analysis of the CYP21A2 gene with intergenic recombination and multiple gene deletions in the RCCX module. | Chang SF | Genetic testing and molecular biomarkers | 2011 | PMID: 21117955 |
Novel deletion alleles carrying CYP21A1P/A2 chimeric genes in Brazilian patients with 21-hydroxylase deficiency. | Coeli FB | BMC medical genetics | 2010 | PMID: 20587039 |
H62L Mutation of CYP21A2 Identified in the Non-classical Form of 21-Hydroxylase Deficiency. | Nagasaki K | Clinical pediatric endocrinology : case reports and clinical investigations : official journal of the Japanese Society for Pediatric Endocrinology | 2009 | PMID: 23926370 |
Inhibition of CYP21A2 enzyme activity caused by novel missense mutations identified in Brazilian and Scandinavian patients. | Soardi FC | The Journal of clinical endocrinology and metabolism | 2008 | PMID: 18381579 |
p.H62L, a rare mutation of the CYP21 gene identified in two forms of 21-hydroxylase deficiency. | Menassa R | The Journal of clinical endocrinology and metabolism | 2008 | PMID: 18319307 |
Low frequency of the CYP21A2 deletion in ethnic Chinese (Taiwanese) patients with 21-hydroxylase deficiency. | Lee HH | Molecular genetics and metabolism | 2008 | PMID: 18039588 |
Follow-up of 68 children with congenital adrenal hyperplasia due to 21-hydroxylase deficiency: relevance of genotype for management. | Pinto G | The Journal of clinical endocrinology and metabolism | 2003 | PMID: 12788866 |
Non-classical 21-hydroxylase deficiency in children: association of adrenocorticotropic hormone-stimulated 17-hydroxyprogesterone with the risk of compound heterozygosity with severe mutations. | Ezquieta B | Acta paediatrica (Oslo, Norway : 1992) | 2002 | PMID: 12222711 |
Mutation analysis in patients with congenital adrenal hyperplasia in the Spanish population: identification of putative novel steroid 21-hydroxylase deficiency alleles associated with the classic form of the disease. | Lobato MN | Human heredity | 1999 | PMID: 10364682 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP21A2 | - | - | - | - |
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Text-mined citations for rs9378252 ...
HelpRecord last updated Nov 03, 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.
NCBI staff reviewed the sequence information reported in PubMed 18319307 to determine the location of this allele on the current reference sequence.