rs6475

Positions:

• chr6-32039426-T-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM1 PP5 BP4

The NM_000500.9(CYP21A2):​c.518T>A​(p.Ile173Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00119 in 151,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0012 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00049 (3 hom.)
  • Failed GnomAD Quality Control
• Consequence: CYP21A2 NM_000500.9 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:20 U:1 O:1
• Conservation: PhyloP100: 2.91

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM1: In a helix (size 17) in uniprot entity CP21A_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_000500.9
• PP5: Variant 6-32039426-T-A is Pathogenic according to our data. Variant chr6-32039426-T-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 12150.We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=1, Uncertain_significance=1, Pathogenic=18}. Variant chr6-32039426-T-A is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (MetaRNN=0.36651677). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A2	NM_000500.9	c.518T>A	p.Ile173Asn	missense_variant	4/10	ENST00000644719.2	NP_000491.4
CYP21A2	NM_001128590.4	c.428T>A	p.Ile143Asn	missense_variant	3/9		NP_001122062.3
CYP21A2	NM_001368143.2	c.113T>A	p.Ile38Asn	missense_variant	4/10		NP_001355072.1
CYP21A2	NM_001368144.2	c.113T>A	p.Ile38Asn	missense_variant	3/9		NP_001355073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP21A2	ENST00000644719.2	c.518T>A	p.Ile173Asn	missense_variant	4/10		NM_000500.9	ENSP00000496625	P1

Frequencies

GnomAD3 genomes AF: 0.00119 AC: 181 AN: 151628 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00158

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00108

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.000481 AC: 120 AN: 249434 Hom.: 0 AF XY: 0.000378 AC XY: 51 AN XY: 135044

Gnomad AFR exome AF: 0.000376

Gnomad AMR exome AF: 0.000466

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000819

Gnomad SAS exome AF: 0.000296

Gnomad FIN exome AF: 0.00125

Gnomad NFE exome AF: 0.000390

Gnomad OTH exome AF: 0.000492

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000492 AC: 718 AN: 1457878 Hom.: 3 Cov.: 58 AF XY: 0.000483 AC XY: 350 AN XY: 725184

Gnomad4 AFR exome AF: 0.000300

Gnomad4 AMR exome AF: 0.000494

Gnomad4 ASJ exome AF: 0.000307

Gnomad4 EAS exome AF: 0.000908

Gnomad4 SAS exome AF: 0.000500

Gnomad4 FIN exome AF: 0.00220

Gnomad4 NFE exome AF: 0.000406

Gnomad4 OTH exome AF: 0.000531

GnomAD4 genome AF: 0.00119 AC: 180 AN: 151748 Hom.: 0 Cov.: 31 AF XY: 0.00128 AC XY: 95 AN XY: 74224

Gnomad4 AFR AF: 0.00104

Gnomad4 AMR AF: 0.00157

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.000415

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.00108

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.000750 Hom.: 0

ExAC AF: 0.000362 AC: 44

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:20 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Pathogenic:11 Uncertain:1 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000012150, PMID:3257825, PS1_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 24671123, PS3_S). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.766, PP3_P). A missense variant is a common mechanism associated with Hyperandrogenism (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000577, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Oct 31, 2018	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 01, 1997	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 17, 2023	Based on the classification scheme VCGS_Germline_v1.3.2, 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. (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to asparagine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v3) <0.01 for a recessive condition (181 heterozygotes, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated cytochrome P450 domain (NCBI, PDB). (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. The variant has previously been reported in many patients with congenital adrenal hyperplasia (ClinVar, HGMD, PMID: 3257825, PMID: 31586465). (SP) 1206 - This variant has been shown to be paternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 20, 2019	NM_000500.7(CYP21A2):c.518T>A(I173N) is classified as pathogenic in the context of congenital adrenal hyperplasia and is associated with the classic form of the disease. Sources cited for classification include the following: PMID 24667412, 21098686, 24671123, 23359698, 22270556, 19750867 and 3257825. Classification of NM_000500.7(CYP21A2):c.518T>A(I173N) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Provincial Medical Genetics Program of British Columbia, University of British Columbia	Jan 01, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	Nov 21, 2018	- -
Pathogenic, no assertion criteria provided	clinical testing	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	Oct 30, 2023	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Apr 04, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Lifecell International Pvt. Ltd	-	This variant in exon 4 of the CYP21A2 gene results in the amino acid substitution from Isoleucine to Asparagine at codon 173 (p.Ile173Asn) with the sequence change of c.518T>A (NM_000500.7). This variant was observed in a proband with increased level of 17-OHP enzyme (86.9 nmol/L) which was screened for advanced newborn screening with confirmatory genetic reflex testing at lifecell diagnostics. The observed variant has a minor allele frequency of 0.000798722 and 0.0005771 in the 1000G database and gnomAD database respectively. The nucleotide is predicted conserved by GERP++ and PhyloP and the in-silico predictions by MutationTaster and SIFT are damaging. This variant lies in the p450 domain of CP21A_HUMAN protein (http://pfam.xfam.org/protein/P08686). This variant (also referred as Ile172Asn) has been previously reported for congenital adrenal hyperplasia (Amor et al., 1988;PMID: 3257825, Speiser et al., 1992;PMID: 1644925, New et al., 2013;PMID: 23359698). Experimental studies have shown that this variant results in abnormal protein function (Tusie-Luna et al., 1990;PMID: 2249999, Chiou et al., 1990;PMID: 2303461, Brønstad et al., 2014;PMID: 24671123). -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Mar 05, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genomic Research Center, Shahid Beheshti University of Medical Sciences	Mar 05, 2018	- -

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 20, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Nov 09, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 20, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 31, 2022	This sequence change replaces isoleucine, which is neutral and non-polar, with asparagine, which is neutral and polar, at codon 173 of the CYP21A2 protein (p.Ile173Asn). 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 classic salt-wasting, simple virilizing, and non-classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency (PMID: 3257825, 8698338, 23359698, 26804566, 30968594). 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 I172N. ClinVar contains an entry for this variant (Variation ID: 12150). 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 expected to disrupt CYP21A2 protein function. Experimental studies have shown that this missense change affects CYP21A2 function (PMID: 2249999, 30968594). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 22, 2023	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. This variant is also referred to as p.Ile172Asn 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. Experiments demonstrate this variant results in dramatically reduced enzymatic activity (PMID: 2249999, 24667412, 24671123). -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Aug 22, 2023	The CYP21A2 c.518T>A (p.Ile173Asn) variant (also known as I173N or I172N) has been reported in the published literature in individuals affected with the classic salt-wasting, simple virilizing, and non-classic forms of CAH (PMIDs: 3257825 (1988), 17042033 (2006), 21098686 (2011), 23359698 (2013), 31586465 (2020)). In addition, experimental studies indicate this variant is damaging to protein function (PMIDs: 2249999 (1990), 24667412 (2014), 24671123 (2014)). The frequency of this variant in the general population, 0.0016 (41/25010 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is consistent with pathogenicity. Based on the available information, this variant is classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Aug 18, 2022	- -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 07, 2014

- -

Congenital adrenal hyperplasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 15, 2023

Variant summary: CYP21A2 c.518T>A (p.Ile173Asn, aka. I172N) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00048 in 249434 control chromosomes (gnomAD). c.518T>A has been reported in the literature in numerous homozygous and compound heterozygous individuals affected with the classic salt-wasting, simple virilizing, and non-classic forms of Congenital Adrenal Hyperplasia (see e.g. Amor_1988, Dolzan_2005, Simonetti_2018, Xu_2019). These data indicate that the variant is very likely to be associated with disease. Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated severely reduced enzyme activity (e.g. Tusie-Luna_1990, Chiou_1990, Xu_2019). 13 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after, and all laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.066	T
BayesDel_noAF	Uncertain	0.060
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.21	.;.;.;T;.;.
Eigen	Pathogenic	0.75
Eigen_PC	Uncertain	0.66
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Benign	0.73	.;.;T;T;.;.
M_CAP	Uncertain	0.29	D
MetaRNN	Benign	0.37	T;T;T;T;T;T
MetaSVM	Uncertain	0.38	D
MutationTaster	Benign	1.0	A;A
PrimateAI	Uncertain	0.66	T
PROVEAN	Pathogenic	-5.5	D;.;D;D;D;.
REVEL	Pathogenic	0.77
Sift	Uncertain	0.0050	D;.;D;D;D;.
Sift4G	Uncertain	0.017	D;.;D;D;D;.
Polyphen		1.0	D;D;.;.;.;D
Vest4		0.97
MVP		0.98
MPC		1.8
ClinPred		0.14	T
GERP RS		5.0
gMVP		0.94

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

Other links and lift over

dbSNP: rs6475; hg19: chr6-32007203; COSMIC: COSV64482986; COSMIC: COSV64482986;