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NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency

Germline classification:
Conflicting interpretations of pathogenicity (13 submissions)
Last evaluated:
Apr 4, 2024
Review status:
criteria provided, conflicting classifications
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000012933.21

Allele description

NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn)

Genes:
LOC106780800:CYP21A2 recombination region [Gene]
CYP21A2:cytochrome P450 family 21 subfamily A member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
6p21.33
Genomic location:
Preferred name:
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn)
Other names:
I172N; rs6475
HGVS:
  • NC_000006.12:g.32039426T>A
  • NG_007941.3:g.6122T>A
  • NG_008337.2:g.74949A>T
  • NG_045215.1:g.1655T>A
  • NM_000500.9:c.518T>AMANE SELECT
  • NM_001128590.4:c.428T>A
  • NM_001368143.2:c.113T>A
  • NM_001368144.2:c.113T>A
  • NP_000491.4:p.Ile173Asn
  • NP_001122062.3:p.Ile143Asn
  • NP_001355072.1:p.Ile38Asn
  • NP_001355073.1:p.Ile38Asn
  • LRG_829t1:c.518T>A
  • LRG_829:g.6122T>A
  • LRG_829p1:p.Ile173Asn
  • NC_000006.11:g.32007203T>A
  • NG_007941.2:g.6119T>A
  • NM_000500.2:c.518T>A
  • NM_000500.5:c.518T>A
  • NM_000500.7:c.518T>A
Protein change:
I143N; ILE172ASN
Links:
OMIM: 613815.0001; dbSNP: rs6475
NCBI 1000 Genomes Browser:
rs6475
Molecular consequence:
  • NM_000500.9:c.518T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128590.4:c.428T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368143.2:c.113T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001368144.2:c.113T>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
4

Condition(s)

Name:
Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Synonyms:
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency; CYP21 deficiency; 21-Hydroxylase-Deficient Congenital Adrenal Hyperplasia
Identifiers:
MONDO: MONDO:0008728; MedGen: C2936858; Orphanet: 90794; OMIM: 201910

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000033174OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 1997)
germlineliterature only

PubMed (8)
[See all records that cite these PMIDs]

SCV000086799GeneReviews
no classification provided
not providedunknownliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000784270Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 5, 2018)
inheritedclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000784271Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 5, 2018)
inheritedclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000883113Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 21, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000893712Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 31, 2018)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001194146Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Dec 20, 2019)
unknownclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Citation Link,

SCV001482475Lifecell International Pvt. Ltd
no assertion criteria provided
Pathogenicgermlineclinical testing

SCV0020590273billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:3257825,

SCV002320854Provincial Medical Genetics Program of British Columbia, University of British Columbia
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002767610Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 15, 2020)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004099489Zotz-Klimas Genetics Lab, MVZ Zotz Klimas
no assertion criteria provided
Pathogenic
(Oct 30, 2023)
germlineclinical testing

SCV004810194Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Apr 4, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot provided1not providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedno2not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

A missense mutation at Ile172----Asn or Arg356----Trp causes steroid 21-hydroxylase deficiency.

Chiou SH, Hu MC, Chung BC.

J Biol Chem. 1990 Feb 25;265(6):3549-52.

PubMed [citation]
PMID:
2303461
See all PubMed Citations (17)
PMC

Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL.

Genetics in medicine : official journal of the American College of Medical Genetics. 2015 Mar 5; 17(5): 405-424

PMC [article]
PMCID:
PMC4544753
PMID:
25741868
DOI:
10.1038/gim.2015.30

Details of each submission

From OMIM, SCV000033174.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (8)

Description

Most mutations in the CYP21 gene causing congenital adrenal hyperplasia (201910) are deletions. Amor et al. (1988) reported the cloning and characterization of a nondeleted mutant CYP21B gene. Codon 172 of the mutant gene was found to be changed from ATC, encoding isoleucine, to AAC, encoding asparagine. This mutation (I172N) is normally present in the CYP21A pseudogene, so that it may have been transferred to the mutant CYP21B gene by gene conversion. Hybridization of oligonucleotide probes corresponding to this and 2 other mutations normally present in CYP21A demonstrated that 4 out of 20 patients carried the codon 172 mutation; in 1 of these patients, the mutation was present as part of a larger gene conversion involving at least exons 3-6. Gene conversion may be a frequent cause of 21-hydroxylase deficiency alleles due to the presence of 6 chi-like sequences (GCTGGGG) in the CYP21 genes and the close proximity of the CYP21A pseudogene, which has several potentially deleterious mutations. Chiou et al. (1990) also found this mutation on 1 allele in a compound heterozygote. Partanen and Campbell (1991) amplified the full-length genomic P450C21 gene by PCR. The ile172-to-asn mutation in exon 4 was demonstrated. This mutation was observed also by Wedell et al. (1992), who referred to it as ILE173ASN. Speiser et al. (1992) found this mutation in 16% of 88 families with congenital adrenal hyperplasia due to 21-hydroxylase deficiency. The mutation falls into their group B with 2% enzyme activity and a simple virilizing phenotype. Among 127 patients with 21-hydroxylase deficiency in Sweden, Wedell et al. (1994) found that the ile173-to-asn mutation accounted for 20.8% of 186 unrelated chromosomes. (In the same study, the CYP21 gene was completely absent in 29.8% of chromosomes, the val281-to-leu mutation accounted for 5.4%, and the arg356-to-trp mutation accounted for 3.8%. The most frequent nondeletional mutation was the splice mutation in intron 2, which accounted for 27.7% of the chromosomes.) This mutation is found in 28% of all the cases of simple virilizing type (White et al., 1994). To clarify the molecular basis of nonclassic CAH detectable by neonatal screening in Japan, Tajima et al. (1997) identified 2 sibs and 2 unrelated newborns who were diagnosed with probable nonclassic steroid 21-hydroxylase deficiency. The 2 sibs were found to have 1 allele that had 2 mutations, ile172 to asn and arg356 to trp.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000086799.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providedAssert pathogenicitynot providednot providednot providednot provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784270.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritednonot providednot providednot provided1not providednot providednot provided

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784271.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritednonot providednot providednot provided1not providednot providednot provided

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV000883113.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV000893712.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Myriad Genetics, Inc., SCV001194146.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Lifecell International Pvt. Ltd, SCV001482475.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing
(GTR000592409)
not provided

Description

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).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided
(GTR000592409)
1not providednot providednot provided

From 3billion, SCV002059027.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Provincial Medical Genetics Program of British Columbia, University of British Columbia, SCV002320854.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767610.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

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 (166 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 (18G00267). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004099489.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810194.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 7, 2024