6-32040421-C-T

Position:

• chr6-32040421-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000500.9(CYP21A2):​c.955C>T​(p.Gln319*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000896 in 1,580,252 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: 𝑓 0.0038 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00062 (0 hom.)
• Consequence: CYP21A2 NM_000500.9 stop_gained
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:25 O:1
• Conservation: PhyloP100: 0.664

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]

CYP21A2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 6-32040421-C-T is Pathogenic according to our data. Variant chr6-32040421-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 12169.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-32040421-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP21A2	NM_000500.9	c.955C>T	p.Gln319*	stop_gained	8/10	ENST00000644719.2	NP_000491.4
CYP21A2	NM_001128590.4	c.865C>T	p.Gln289*	stop_gained	7/9		NP_001122062.3
CYP21A2	NM_001368143.2	c.550C>T	p.Gln184*	stop_gained	8/10		NP_001355072.1
CYP21A2	NM_001368144.2	c.550C>T	p.Gln184*	stop_gained	7/9		NP_001355073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP21A2	ENST00000644719.2	c.955C>T	p.Gln319*	stop_gained	8/10		NM_000500.9	ENSP00000496625.1

Frequencies

GnomAD3 genomes AF: 0.00382 AC: 523 AN: 136986 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00331

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00419

Gnomad ASJ AF: 0.00878

Gnomad EAS AF: 0.00236

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.000399

Gnomad MID AF: 0.0534

Gnomad NFE AF: 0.00346

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.000622 AC: 898 AN: 1443134 Hom.: 0 Cov.: 38 AF XY: 0.000684 AC XY: 491 AN XY: 717354

Gnomad4 AFR exome AF: 0.000491

Gnomad4 AMR exome AF: 0.000907

Gnomad4 ASJ exome AF: 0.00292

Gnomad4 EAS exome AF: 0.000153

Gnomad4 SAS exome AF: 0.000713

Gnomad4 FIN exome AF: 0.000154

Gnomad4 NFE exome AF: 0.000534

Gnomad4 OTH exome AF: 0.00141

GnomAD4 genome AF: 0.00378 AC: 518 AN: 137118 Hom.: 0 Cov.: 33 AF XY: 0.00381 AC XY: 255 AN XY: 67010

Gnomad4 AFR AF: 0.00333

Gnomad4 AMR AF: 0.00419

Gnomad4 ASJ AF: 0.00878

Gnomad4 EAS AF: 0.00237

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.000399

Gnomad4 NFE AF: 0.00346

Gnomad4 OTH AF: 0.0108

Alfa AF: 0.00853 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:25 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency Pathogenic:13 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 17, 2019	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Pittsburgh Clinical Genomics Laboratory, University of Pittsburgh Medical Center	Jun 28, 2023	This sequence variant is a single nucleotide substitution (C>T) in exon 8 of 10 of the CYP21A2 gene that changes the glutamine codon at position 319 to an early termition sigl. This variant may be referred to as Q318X in the literature. This variant is predicted to generate a non-functiol allele through either the expression of a truncated protein or a loss of CYP21A2 expression due to nonsense mediated decay. This is a previously reported variant (ClinVar 12169) that is one of the most commonly observed alleles observed in individuals affected by non-classical, simple virilizing, or salt wasting forms of congenital adrel hyperplasia due to 21-hydroxylase deficiency when in the homozygous, hemizygous, or compound heterozygous states (PMID: 3267225, 31446012, 23142378, 23359698, 26804566). This variant is present in 100 of 277730 alleles (0.0360%) in the gnomAD population dataset. A functiol study has confirmed that mR of this variant is rapidly degraded when expressed in mammalian cells (PMID: 3267225). Based upon the evidence, we consider this variant to be pathogenic. ACMG Criteria: PM3, PS4, PVS1 -
Pathogenic, no assertion criteria provided	clinical testing	Lifecell International Pvt. Ltd	-	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). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 01, 2002	- -
Pathogenic, criteria provided, single submitter	research	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 17, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	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. -
Pathogenic, no assertion criteria provided	clinical testing	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	Apr 27, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	May 22, 2022	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. -
Pathogenic, criteria provided, single submitter	clinical testing	DASA	Mar 05, 2022	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Dec 19, 2019	This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	research	Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital	Oct 04, 2024	PVS1,PS3,PM3 -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 16, 2023	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 -

not provided Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jun 24, 2024	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)). In multiple individuals with clinical features associated with this gene, this variant has been seen in trans with other recessive pathogenic variants in CYP21A2, suggesting this variant is also pathogenic. In some published literature, this variant is referred to as p.Q318X. Assessment of experimental evidence suggests this variant results in abnormal protein function. (PMID: 3267225) -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Nov 24, 2015	- -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jun 07, 2023	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 03, 2017	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 02, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Mar 24, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Nov 03, 2022	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. -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Aug 18, 2022	- -

CYP21A2-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 12, 2024

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. -

Congenital adrenal hyperplasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Mar 20, 2022

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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	37
DANN	Uncertain	1.0
Eigen	Pathogenic	0.96
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Uncertain	0.78	D
Vest4		0.83
GERP RS		5.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs7755898; hg19: chr6-32008198; COSMIC: COSV64480175; COSMIC: COSV64480175;