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rs12948217

From SNPedia

Canavan disease
Orientationplus
Stabilizedplus
Geno Mag Summary
(A;A) 8 Canavan disease (predicted); note issue with microarray data though
(A;C) 3 Carrier of a Canavan disease mutation; note issue with microarray data though
(A;T) 3 Carrier of a Canavan disease mutation
(C;C) 0 common in clinvar
(C;T) 0
(T;T) 0
ReferenceGRCh38 38.1/141
Chromosome17
Position3494408
GeneASPA, SPATA22
is asnp
is mentioned by
dbSNPrs12948217
dbSNP (classic)rs12948217
ClinGenrs12948217
ebirs12948217
HLIrs12948217
Exacrs12948217
Gnomadrs12948217
Varsomers12948217
LitVarrs12948217
Maprs12948217
PheGenIrs12948217
Biobankrs12948217
1000 genomesrs12948217
hgdprs12948217
ensemblrs12948217
geneviewrs12948217
scholarrs12948217
googlers12948217
pharmgkbrs12948217
gwascentralrs12948217
openSNPrs12948217
23andMers12948217
23andMe allrs12948217
SNPshotrs12948217
SNPdbers12948217
MSV3drs12948217
GWAS Ctlgrs12948217
GMAF0.208
Max Magnitude8
OMIM608034
DescCanavan disease
Variant0005
Relatedalso

rs12948217, also known as c.693C>A, Y231X or Tyr231Ter, is a SNP in the ASPA gene. Note that a benign variant of this SNP (c.693C>T) also exists as discussed below.


Only the A allele at rs12948217 confers risk to Canavan disease. A person with the CC, CT, or TT alleles is not a carrier; someone with the AC or AT alleles is a carrier; and people with two AA alleles are affected with the disease.

Note that due for technical reasons, the vast majority of direct-to-consumer companies using DNA chips (microarrays) for genotyping do not distinguish the benign T allele from the pathogenic A allele. As a result, raw data from these companies that reports (A;C) and especially (A;A) is quite likely to actually represent the benign (C;T) or perhaps (T;T) genotypes. This type of error applies only to data derived from microarrays (specifically, Illumina microarrays such as those used by 23andMe and Ancestry) and does not apply to data generated by sequencing.


ClinVar
Risk Rs12948217(A;A) Rs12948217(T;T)
Alt Rs12948217(A;A) Rs12948217(T;T)
Reference Rs12948217(C;C)
Significance Pathogenic
Disease Spongy degeneration of central nervous system not specified
Variation info
Gene SPATA22 ASPA
CLNDBN Spongy degeneration of central nervous system not specified
Reversed 0
HGVS NC_000017.10:g.3397702C>A; NC_000017.10:g.3397702C>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000002727.5, RCV000178705.2, RCV000297817.1,



[PMID 18974781OA-icon.png] Cataloging coding sequence variations in human genome databases.