rs6445

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PP5_Very_StrongBP4

The NM_000500.9(CYP21A2):​c.1360C>T​(p.Pro454Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00628 in 1,223,580 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.0051 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0065 ( 3 hom. )

Consequence

CYP21A2
NM_000500.9 missense

Scores

2
8
5

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:28O:1

Conservation

PhyloP100: 0.697
Variant links:
Genes affected
CYP21A2 (HGNC:2600): (cytochrome P450 family 21 subfamily A member 2) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This protein localizes to the endoplasmic reticulum and hydroxylates steroids at the 21 position. Its activity is required for the synthesis of steroid hormones including cortisol and aldosterone. Mutations in this gene cause congenital adrenal hyperplasia. A related pseudogene is located near this gene; gene conversion events involving the functional gene and the pseudogene are thought to account for many cases of steroid 21-hydroxylase deficiency. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PP5
Variant 6-32041006-C-T is Pathogenic according to our data. Variant chr6-32041006-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 12159.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-32041006-C-T is described in Lovd as [Pathogenic].
BP4
Computational evidence support a benign effect (MetaRNN=0.013331294). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CYP21A2NM_000500.9 linkuse as main transcriptc.1360C>T p.Pro454Ser missense_variant 10/10 ENST00000644719.2 NP_000491.4
CYP21A2NM_001128590.4 linkuse as main transcriptc.1270C>T p.Pro424Ser missense_variant 9/9 NP_001122062.3
CYP21A2NM_001368143.2 linkuse as main transcriptc.955C>T p.Pro319Ser missense_variant 10/10 NP_001355072.1
CYP21A2NM_001368144.2 linkuse as main transcriptc.955C>T p.Pro319Ser missense_variant 9/9 NP_001355073.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CYP21A2ENST00000644719.2 linkuse as main transcriptc.1360C>T p.Pro454Ser missense_variant 10/10 NM_000500.9 ENSP00000496625 P1

Frequencies

GnomAD3 genomes
AF:
0.00509
AC:
771
AN:
151528
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00167
Gnomad AMI
AF:
0.0132
Gnomad AMR
AF:
0.00334
Gnomad ASJ
AF:
0.000866
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00172
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.00899
Gnomad OTH
AF:
0.00240
GnomAD3 exomes
AF:
0.00460
AC:
633
AN:
137706
Hom.:
2
AF XY:
0.00448
AC XY:
335
AN XY:
74808
show subpopulations
Gnomad AFR exome
AF:
0.00114
Gnomad AMR exome
AF:
0.00320
Gnomad ASJ exome
AF:
0.000365
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000787
Gnomad FIN exome
AF:
0.00296
Gnomad NFE exome
AF:
0.00902
Gnomad OTH exome
AF:
0.00386
GnomAD4 exome
AF:
0.00645
AC:
6916
AN:
1071934
Hom.:
3
Cov.:
16
AF XY:
0.00641
AC XY:
3469
AN XY:
541524
show subpopulations
Gnomad4 AFR exome
AF:
0.00106
Gnomad4 AMR exome
AF:
0.00279
Gnomad4 ASJ exome
AF:
0.000471
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000732
Gnomad4 FIN exome
AF:
0.00219
Gnomad4 NFE exome
AF:
0.00811
Gnomad4 OTH exome
AF:
0.00504
GnomAD4 genome
AF:
0.00508
AC:
771
AN:
151646
Hom.:
0
Cov.:
33
AF XY:
0.00463
AC XY:
343
AN XY:
74058
show subpopulations
Gnomad4 AFR
AF:
0.00166
Gnomad4 AMR
AF:
0.00334
Gnomad4 ASJ
AF:
0.000866
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00172
Gnomad4 NFE
AF:
0.00900
Gnomad4 OTH
AF:
0.00238
Alfa
AF:
0.00466
Hom.:
0
ExAC
AF:
0.000962
AC:
85

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:28Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:13
Pathogenic, criteria provided, single submitterclinical testingAiLife Diagnostics, AiLife DiagnosticsJun 02, 2021- -
Pathogenic, criteria provided, single submitterclinical testingInstitute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU DresdenNov 03, 2021- -
Pathogenic, no assertion criteria providedclinical testingJoint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+-- -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 01, 2022This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 454 of the CYP21A2 protein (p.Pro454Ser). 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 missense change has been observed in individual(s) with clinical features of non-classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency (PMID: 1406699, 10720040, 12222711, 12887291, 21444649, 21843885, 22270556, 23073904, 31333583, 32966723). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as P453S. ClinVar contains an entry for this variant (Variation ID: 12159). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CYP21A2 protein function. Experimental studies have shown that this missense change affects CYP21A2 function (PMID: 18381579, 24953648, 30968594). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingClinical Genetics and Genomics, Karolinska University HospitalMay 19, 2016- -
Pathogenic, criteria provided, single submitterclinical testingQuest Diagnostics Nichols Institute San Juan CapistranoMar 13, 2023The variant seen in patients with salt-wasting phenotype (PMID: 12788866 (2003)) and simple virilizing phenotype (PMID: 18381579 (2008)). 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. -
Pathogenic, criteria provided, single submitterclinical testingAthena DiagnosticsMar 13, 2023Frequency 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 reported to associate with non-classic congenital adrenal hyperplasia (CAH). This variant is also referred to as p.Pro453Ser (P453S) in published literature. 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. This variant results in reduced enzymatic activity (PMID: 24953648). -
Pathogenic, criteria provided, single submitterclinical testingClinical Genetics Laboratory, Skane University Hospital LundMay 27, 2022- -
Pathogenic, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityAug 04, 2023- -
Pathogenic, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, Amsterdam University Medical Center-- -
Pathogenic, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Pathogenic, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Dec 29, 2014- -
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Pathogenic:12Other:1
Pathogenic, criteria provided, single submittercurationLaboratory of Medical Genetics, National & Kapodistrian University of AthensFeb 01, 2024- -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsOct 18, 2021- -
Pathogenic, criteria provided, single submitterclinical testingVictorian Clinical Genetics Services, Murdoch Childrens Research InstituteMay 06, 2021Based 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 nonclassic type hyperandrogenism due to 21-hydroxylase deficiency (MIM#201910). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from proline to serine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 757 heterozygotes, 2 homozygotes). (SP) 0504 - Same amino acid change has been observed in placental mammals. (SB) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It is regarded as definitely pathogenic by EMQN (PMID: 32616876) and is associated to the nonclassic type of hyperandrogenism due to 21-hydroxylase deficiency (ClinVar, LOVD, PMID: 31586465). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Likely pathogenic, criteria provided, single submitterclinical testing3billionSep 01, 2022It is observed in the gnomAD v2.1.1 ( https://gnomad.broadinstitute.org ) dataset at total allele frequency of 0.453%. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.45; 3Cnet: 0.88). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012159). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, no assertion criteria providedcurationReproductive Health Research and Development, BGI GenomicsJan 06, 2020NM_000500.7:c.1360C>T in the CYP21A2 gene has an allele frequency of 0.009 in European (non-Finnish) subpopulation in the gnomAD database. The c.1360C>T (p.Pro454Ser) missense variant in the CYP21A2 gene, also known as p.Pro453Ser in literatures, has been previously found in 46.2% of 13 unrelated NC-CAH patients, but only 7.7% and 3.6% of salt-wasting CAH patients and blood donors, respectively (PMID: 1406699). In vitro functional assays in multiple studies demonstrated that, compared to the wild-type enzyme, this variant had decreased activity on both the 17-OHP and progesterone substrates (PMID: 24953648). Pathogenic computational verdict because pathogenic predictions from DANN, EIGEN, FATHMM-MKL, M-CAP, MutationTaster and SIFT. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PP3, PS4, PS3. -
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 01, 2008- -
Pathogenic, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsOct 31, 2018- -
Pathogenic, criteria provided, single submitterclinical testingIntergen, Intergen Genetics and Rare Diseases Diagnosis CenterJul 26, 2023- -
Pathogenic, criteria provided, single submitterresearchUNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill-The CYP21A2 c.1360C>T (p.P454S) missense variant has been reported in individuals with nonclassical late-onset 21-hydroxylase deficiency (PMID: 1406699; 18381579; 1496017). -
Pathogenic, criteria provided, single submitterclinical testingKnight Diagnostic Laboratories, Oregon Health and Sciences UniversityJul 18, 2016The c.1360C>T (p.Pro454Ser) missense variant in the CYP21A2 gene has been previously reported in multiple individuals affected with 21-OHD CAH and is associated with the non-classic form of this disorder (Owerbach et al., 1992; Vigliani and Buster, 2012; Skordis et al., 2015; Neocleous et al., 2014). This variant is present significantly more frequently in affected individuals than controls (OR = 18; 95%CI = 2.37-136), and is absent or reported at low frequency in the population databases (Exome Sequencing Project [ESP]; 1000 Genomes=0.6%; ExAC=0.88%). Furthermore, in vitro functional assays in multiple studies demonstrated that, compared to the wild-type enzyme, this variant had decreased activity on both the 17-OHP and progesterone substrates (Nikoshkov et al., 1997, Barbaro et al., 2015). Structural studies predict that Pro454 is positioned within a hydrophobic pocket, and that the p.Pro454Ser variant will disrupt the hydrophobicity of this region (Haider et al., 2013). In addition, Emory Genetics Laboratory has classified this variant as Pathogenic. Pathogenic variants in the CYP21A2 gene are the only known cause of 21-OHD CAH. Therefore, this collective evidence supports the classification of the c.1360C>T (p.Pro454Ser) as a Pathogenic variant for congenital adrenal hyperplasia. We have confirmed this finding in our laboratory using Sanger sequencing. -
Pathogenic, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpJun 29, 2022Variant summary: CYP21A2 c.1360C>T (p.Pro454Ser) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0046 in 137706 control chromosomes in the gnomAD database, including 2 homozygotes. This frequency is not significantly higher than expected for a pathogenic variant in CYP21A2 causing Congenital Adrenal Hyperplasia/Non-Classic (0.0046 vs 0.032), allowing no conclusion about variant significance. c.1360C>T has been reported in the literature in multiple individuals affected with Congenital Adrenal Hyperplasia. These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in 10%-<30% of normal activity (Helmberg_1992, Nikoshkov_1997, Soardi_2008). Ten 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. -
Pathogenic, criteria provided, single submitterclinical testingMendelicsMay 04, 2022- -
not provided, no classification providedliterature onlyGeneReviews-- -
CYP21A2-related disorder Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesSep 23, 2024The CYP21A2 c.1360C>T variant is predicted to result in the amino acid substitution p.Pro454Ser. This variant is associated with autosomal recessive non-classic congenital adrenal hyperplasia (CAH) (also known as P453S; New et al. 2006. PubMed ID: 16912124; Nikoshkov et al. 1997. PubMed ID: 8989258; Soardi et al. 2008. PubMed ID: 18381579). This is a common deleterious variant, which likely originated from the pseudogene CYP21A1P via gene conversion. This variant is interpreted as pathogenic. -
Congenital lipoid adrenal hyperplasia due to STAR deficency Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingMGZ Medical Genetics CenterJul 26, 2021- -
See cases Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics, University Hospital MuensterAug 19, 2022ACMG categories: PS3,PS4,PM1,PP3,PP5 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
23
DANN
Uncertain
1.0
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.26
FATHMM_MKL
Uncertain
0.82
D
M_CAP
Pathogenic
0.83
D
MetaRNN
Benign
0.013
T;T;T;T
MetaSVM
Benign
-0.47
T
MutationTaster
Benign
0.99
A;A
PrimateAI
Uncertain
0.50
T
PROVEAN
Pathogenic
-5.7
D;.;D;.
REVEL
Uncertain
0.45
Sift
Uncertain
0.0030
D;.;D;.
Sift4G
Uncertain
0.0090
D;.;D;.
Polyphen
0.99
D;D;.;D
Vest4
0.70
MVP
0.71
MPC
0.032
ClinPred
0.036
T
GERP RS
3.7
gMVP
0.75

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6445; hg19: chr6-32008783; COSMIC: COSV64482528; COSMIC: COSV64482528; API