chr6:32039426:T>A Detail (hg38) (CYP21A2, LOC106780800)

Information

Genome

Assembly Position
hg19 chr6:32,007,203-32,007,203 View the variant detail on this assembly version.
hg38 chr6:32,039,426-32,039,426

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000435122.3:c.428T>A ENST00000435122.3:p.Ile143Asn
ENST00000644719.2:c.518T>A ENST00000644719.2:p.Ile173Asn
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 613815 OMIM
HGNC 2600 HGNC
Ensembl ENSG00000231852 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv24809738 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic combined 21-hydroxylase deficiency (21-OHD) germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Pathogenic CHARGE syndrome (CS) germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2024-04-04 criteria provided, conflicting interpretations Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency germline inherited unknown Detail
Pathogenic 2014-09-07 criteria provided, single submitter Inborn genetic diseases germline Detail
Pathogenic 2023-08-22 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Pathogenic 2023-03-15 criteria provided, single submitter congenital adrenal hyperplasia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.294 congenital adrenal hyperplasia To determine RCCX alterations, we used the polymerase chain reaction (PCR) produ... BeFree 21117955 Detail
<0.001 congenital adrenal hyperplasia To determine RCCX alterations, we used the polymerase chain reaction (PCR) produ... BeFree 21117955 Detail
0.042 Chronic active hepatitis Genotyping for the four common mutations (IVS2-13A/C&gt;G, p.Q318X, large lesion... BeFree 18973462 Detail
0.042 Chronic active hepatitis Adult young women with CAH: three with the salt-wasting form and four patients w... BeFree 15136096 Detail
0.005 Virilism Sequencing of the AR gene in five unrelated CAH girls with the I172N mutation in... BeFree 12050225 Detail
0.042 Chronic active hepatitis Sequencing of the AR gene in five unrelated CAH girls with the I172N mutation in... BeFree 12050225 Detail
0.294 congenital adrenal hyperplasia Substitution of Ile-172 to Asn in the steroid 21-hydroxylase B (P450c21B) gene i... BeFree 1937474 Detail
0.042 Chronic active hepatitis To assess the contributions of pre- and postnatal androgens, the CAH subjects we... BeFree 14715880 Detail
0.294 congenital adrenal hyperplasia We hereby describe our recent experience with the pregnancy of a patient who had... BeFree 14664429 Detail
0.155 21-hydroxylase deficiency NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND Classic congenital adrenal hyperplasia due to 21-hyd... ClinVar Detail
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND Inborn genetic diseases ClinVar Detail
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND not provided ClinVar Detail
NM_000500.9(CYP21A2):c.518T>A (p.Ile173Asn) AND Congenital adrenal hyperplasia ClinVar Detail
To determine RCCX alterations, we used the polymerase chain reaction (PCR) product containing the te... DisGeNET Detail
To determine RCCX alterations, we used the polymerase chain reaction (PCR) product containing the te... DisGeNET Detail
Genotyping for the four common mutations (IVS2-13A/C&gt;G, p.Q318X, large lesions of the CYP21A2 gen... DisGeNET Detail
Adult young women with CAH: three with the salt-wasting form and four patients with simple virilizin... DisGeNET Detail
Sequencing of the AR gene in five unrelated CAH girls with the I172N mutation in CYP21 and minimal v... DisGeNET Detail
Sequencing of the AR gene in five unrelated CAH girls with the I172N mutation in CYP21 and minimal v... DisGeNET Detail
Substitution of Ile-172 to Asn in the steroid 21-hydroxylase B (P450c21B) gene in a Finnish patient ... DisGeNET Detail
To assess the contributions of pre- and postnatal androgens, the CAH subjects were categorized into ... DisGeNET Detail
We hereby describe our recent experience with the pregnancy of a patient who had congenital adrenal ... DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs6475 dbSNP
Genome
hg38
Position
chr6:32,039,426-32,039,426
Variant Type
snv
Reference Allele
T
Alternative Allele
A
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1061
Mean of sample read depth (HGVD)
31.28
Standard deviation of sample read depth (HGVD)
14.88
Number of reference allele (HGVD)
2121
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.71253534401508E-4
Gene Symbol (HGVD)
CYP21A2
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
VQSRTrancheSNP99.60to99.80
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs6475
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
7638
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
101568
Allele Counts in All Race (ExAC)
41
Heterozygous Counts in All Race (ExAC)
41
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
4.0367044738500314E-4
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