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rs61630004

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 1 significance unclear; slight change related to ectodermal dysplasia
(A;G) 1 significance unclear; possibly a carrier for an ectodermal dysplasia allele
(G;G) 0 common in clinvar
ReferenceGRCh38 38.1/142
Chromosome12
Position52367173
GeneKRT85
is asnp
is mentioned by
dbSNPrs61630004
ebirs61630004
HLIrs61630004
Exacrs61630004
Varsomers61630004
Maprs61630004
PheGenIrs61630004
hapmaprs61630004
1000 genomesrs61630004
hgdprs61630004
ensemblrs61630004
gopubmedrs61630004
geneviewrs61630004
scholarrs61630004
googlers61630004
pharmgkbrs61630004
gwascentralrs61630004
openSNPrs61630004
23andMers61630004
23andMe allrs61630004
SNP Nexus

SNPshotrs61630004
SNPdbers61630004
MSV3drs61630004
GWAS Ctlgrs61630004
GMAF0.02663
Max Magnitude1

aka c.233G>A, p.Arg78His and R78H

The rs61630004(A) allele is reported as pathogenic when homozygous (i.e. recessively inherited) for "pure" ectodermal dysplasia in two sets of Pakistani families.[PMID 16525032OA-icon.png], [PMID 19865094OA-icon.png]

However, the minor allele frequency appears to be around 1-3% in most populations, and as GET-Evidence states, this makes it unlikely that (A;A) homozygotes are routinely afflicted by ectodermal dysplasia, since it has an incidence of only around .02-.01% (1 or 2 in 10,000).

OMIM602767
Desc
Variant0001
Relatedalso


ClinVar
Risk rs61630004(A;A)
Alt rs61630004(A;A)
Reference rs61630004(G;G)
Significance Pathogenic
Disease Ectodermal dysplasia not provided
Variation info
Gene KRT85
CLNDBN Ectodermal dysplasia, 'pure' hair-nail type not provided
Reversed 1
HGVS NC_000012.11:g.52760957C>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000007238.3, RCV000056956.1,



GET Evidence
KRT85-R78H
aa_change Arg78His
aa_change_short R78H
impact benign
qualified_impact Low clinical importance, Uncertain benign
overall_frequency 0.042466
summary Presumed benign. Although this variant was implicated in causing ectodermal dysplasia in a recessive manner in two Pakistani families (one of which was large and consanguineous), GET-Evidence reports that the variant has been seen in 5 out of 114 random control chromosomes. This strongly contradicts a severe pathogenic effect.