chr6-32040110-G-T

Variant names:

• chr6-32040110-G-T
• rs6471
• NM_000500.9:c.844G>T

Variant summary

Our verdict is Pathogenic. The variant received 13 ACMG points: 15P and 2B. PS3 PM1 PP2 PP5_Very_Strong BP4 BS2_Supporting

The NM_000500.9(CYP21A2):​c.844G>T​(p.Val282Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.005 in 1,595,168 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). ClinVar reports functional evidence for this variant: "SCV000245595: "In vitro functional studies indicate that the p.Val282Leu variant may impact protein function (Tusie-Luna 1990, Barbaro 2015)."" and additional evidence is available in ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency:
  • Genomes: 𝑓 0.011 (4 hom., cov: 32)
  • Exomes 𝑓: 0.0044 (16 hom.)
• Consequence: CYP21A2 NM_000500.9 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:36 O:1
• Conservation: PhyloP100: 2.60
• Publications: 287 publications found

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 Gene-Disease associations (from GenCC):

• classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Myriad Women’s Health, Laboratory for Molecular Medicine
• classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency, salt wasting form

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency, simple virilizing form

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 13 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV000245595: "In vitro functional studies indicate that the p.Val282Leu variant may impact protein function (Tusie-Luna 1990, Barbaro 2015)."; SCV000494239: Functional studies found that co-expression of this mutant protein and wild-type (WT) protein results in a dominant negative effect on the enzymatic activity of WT protein (Felix-Lopez et al. 2003). Other studies indicate reduced enzyme activity with the p.Val281Leu allele (Wu and Chung 1991, Haider et al. 2013).; SCV001142354: "In vitro functional studies indicate that the p.Val282Leu variant may impact protein function." PMID:24953648; SCV002521256: Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 20661889, 21609351).; SCV003852661: Experimental studies have shown that this missense change affects CYP21A2 function (Karlsson L et al., 2019).; SCV005200514: "backed by functional studies (PS3)."; SCV005416532: "Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product."; SCV000263011: Functional analysis demonstrated that the p.V282L alteration reduces 21-hydroxylase activity by about 50% due to an increase in chain length resulting in relatively modest steric clashes in the I-helix of the protein (Haider, 2013; New, 2013).; SCV000841748: Expression of this variant results in reduced enzymatic activity compared to wild type (PMID: 2249999, 24953648).; SCV001552008: Functional studies have found that the p.Val282Leu variant results in a 20-50% reduction in enzymatic activity (Tusie-Luna_1990_PMID:2249999).; SCV002242900: Experimental studies have shown that this missense change affects CYP21A2 function (PMID: 1864962, 2249999, 31344365).; SCV002051107: The most pronounced variant effect results in 30%-50% of normal activity (White_2000).
• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_000500.9
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 52 curated pathogenic missense variants (we use a threshold of 10). The gene has 5 curated benign missense variants. Trascript score misZ: 1.8021 (below the threshold of 3.09). GenCC associations: The gene is linked to classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency, simple virilizing form, classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency, classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency, salt wasting form.
• PP5: Variant 6-32040110-G-T is Pathogenic according to our data. Variant chr6-32040110-G-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 12151.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.0096589625). . Strength limited to SUPPORTING due to the PP5.
• BS2: High Homozygotes in GnomAd4 at 4 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000500.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP21A2	NM_000500.9	MANE Select	c.844G>T	p.Val282Leu	missense	Exon 7 of 10	NP_000491.4
	CYP21A2	NM_001128590.4		c.754G>T	p.Val252Leu	missense	Exon 6 of 9	NP_001122062.3	P08686-2
	CYP21A2	NM_001368143.2		c.439G>T	p.Val147Leu	missense	Exon 7 of 10	NP_001355072.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CYP21A2	ENST00000644719.2	MANE Select	c.844G>T	p.Val282Leu	missense	Exon 7 of 10	ENSP00000496625.1	P08686-1
	CYP21A2	ENST00000960600.1		c.880G>T	p.Val294Leu	missense	Exon 7 of 10	ENSP00000630659.1
	CYP21A2	ENST00000960597.1		c.853G>T	p.Val285Leu	missense	Exon 7 of 10	ENSP00000630656.1

Frequencies

GnomAD3 genomes AF: 0.0109 AC: 1638 AN: 150884 Hom.: 4 Cov.: 32

Gnomad AFR AF: 0.00485

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0723

Gnomad EAS AF: 0.00213

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00113

Gnomad MID AF: 0.0160

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0245

GnomAD2 exomes AF: 0.00528 AC: 1280 AN: 242232 AF XY: 0.00442

Gnomad AFR exome AF: 0.00295

Gnomad AMR exome AF: 0.0134

Gnomad ASJ exome AF: 0.0233

Gnomad EAS exome AF: 0.000932

Gnomad FIN exome AF: 0.000880

Gnomad NFE exome AF: 0.00447

Gnomad OTH exome AF: 0.00865

GnomAD4 exome AF: 0.00439 AC: 6337 AN: 1444170 Hom.: 16 Cov.: 38 AF XY: 0.00429 AC XY: 3082 AN XY: 718662

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00297 AC: 99 AN: 33278

American (AMR) AF: 0.0149 AC: 661 AN: 44246

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 1126 AN: 24906

East Asian (EAS) AF: 0.000631 AC: 25 AN: 39634

South Asian (SAS) AF: 0.000905 AC: 78 AN: 86152

European-Finnish (FIN) AF: 0.00136 AC: 71 AN: 52258

Middle Eastern (MID) AF: 0.00959 AC: 54 AN: 5628

European-Non Finnish (NFE) AF: 0.00334 AC: 3669 AN: 1098614

Other (OTH) AF: 0.00932 AC: 554 AN: 59454

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0109 AC: 1639 AN: 150998 Hom.: 4 Cov.: 32 AF XY: 0.00968 AC XY: 715 AN XY: 73886

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00486 AC: 201 AN: 41396

American (AMR) AF: 0.0276 AC: 415 AN: 15012

Ashkenazi Jewish (ASJ) AF: 0.0723 AC: 238 AN: 3290

East Asian (EAS) AF: 0.00214 AC: 11 AN: 5150

South Asian (SAS) AF: 0.00125 AC: 6 AN: 4816

European-Finnish (FIN) AF: 0.00113 AC: 12 AN: 10616

Middle Eastern (MID) AF: 0.0174 AC: 5 AN: 288

European-Non Finnish (NFE) AF: 0.0104 AC: 701 AN: 67460

Other (OTH) AF: 0.0242 AC: 50 AN: 2062

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00714 Hom.: 0

ExAC AF: 0.0103 AC: 1240

ClinVar

ClinVar submissions

Significance: Pathogenic/Likely pathogenic

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
19	-	-	ADRENAL HYPERPLASIA, CONGENITAL, DUE TO 21-HYDROXYLASE DEFICIENCY (20)
12	-	-	not provided (12)
1	-	-	Adenoma, cortisol-producing (1)
1	-	-	Carcinoma, adrenocortical, androgen-secreting (1)
1	-	-	Congenital adrenal hyperplasia (1)
1	-	-	CYP21A2-related disorder (1)
1	-	-	Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Uncertain	0.064	T
BayesDel_noAF	Benign	-0.15
CADD	Uncertain	23
DANN	Uncertain	0.99
Eigen	Benign	0.054
Eigen_PC	Benign	0.10
FATHMM_MKL	Uncertain	0.88	D
MetaRNN	Benign	0.0097	T
MetaSVM	Benign	-0.97	T
PhyloP100		2.6
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-0.90	N
REVEL	Uncertain	0.31
Sift	Benign	0.61	T
Sift4G	Benign	0.41	T
Polyphen		0.93	P
Vest4		0.88
MutPred		0.86		Gain of disorder (P = 0.1696)
MPC		1.2
ClinPred		0.98	D
GERP RS		4.0
gMVP		0.60
Mutation Taster		=11/89	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs6471; hg19: chr6-32007887; COSMIC: COSV64479410; COSMIC: COSV64479410;