- This record was updated by the submitter. Please see the current version.
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno 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
This HGVS expression did not pass validation- 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
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000033174 | OMIM | no assertion criteria provided | Pathogenic (Jul 1, 1997) | germline | literature only | |
SCV000086799 | GeneReviews | no classification provided | not provided | unknown | literature only | |
SCV000784270 | Genomic Research Center, Shahid Beheshti University of Medical Sciences | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 5, 2018) | inherited | clinical testing | |
SCV000784271 | Genomic Research Center, Shahid Beheshti University of Medical Sciences | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 5, 2018) | inherited | clinical testing | |
SCV000883113 | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Nov 21, 2018) | unknown | clinical testing | |
SCV000893712 | Fulgent Genetics, Fulgent Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 31, 2018) | unknown | clinical testing | |
SCV001194146 | Myriad Genetics, Inc. | criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019)) | Pathogenic (Dec 20, 2019) | unknown | clinical testing | |
SCV001482475 | Lifecell International Pvt. Ltd | no assertion criteria provided | Pathogenic | germline | clinical testing | |
SCV002059027 | 3billion | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 3, 2022) | germline | clinical testing | PubMed (1) PMID:3257825, |
SCV002320854 | Provincial Medical Genetics Program of British Columbia, University of British Columbia | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jan 1, 2022) | germline | clinical testing | |
SCV002767610 | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
| criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Oct 15, 2020) | germline | clinical testing | |
SCV004099489 | Zotz-Klimas Genetics Lab, MVZ Zotz Klimas | no assertion criteria provided | Pathogenic (Oct 30, 2023) | germline | clinical testing | |
SCV004810194 | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Uncertain significance (Apr 4, 2024) | germline | clinical testing |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | germline | yes | 2 | not provided | not provided | 1 | not provided | clinical testing |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | inherited | no | 2 | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | unknown | not provided | not provided | not provided | not provided | not provided | not provided | literature 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.
- PMID:
- 2303461
Partanen J, Campbell RD.
Hum Genet. 1991 Oct;87(6):716-20.
- PMID:
- 1937474
PMC
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
- PMCID:
- PMC4544753
- PMID:
- 25741868
- DOI:
- 10.1038/gim.2015.30
Details of each submission
From OMIM, SCV000033174.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV000086799.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | not provided | not provided | not provided | Assert pathogenicity | not provided | not provided | not provided | not provided |
From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784270.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | no | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784271.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | no | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV000883113.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Fulgent Genetics, Fulgent Genetics, SCV000893712.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Myriad Genetics, Inc., SCV001194146.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Lifecell International Pvt. Ltd, SCV001482475.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | 1 | not provided | not provided | clinical 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).
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | (GTR000592409) | 1 | not provided | not provided | not provided |
From 3billion, SCV002059027.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical 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.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | 1 | not provided | not provided | 1 | not provided | not provided | not provided |
From Provincial Medical Genetics Program of British Columbia, University of British Columbia, SCV002320854.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767610.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical 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
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Zotz-Klimas Genetics Lab, MVZ Zotz Klimas, SCV004099489.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | not provided |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, SCV004810194.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: May 7, 2024