Have questions? Visit https://www.reddit.com/r/SNPedia

rs1494558

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 0 common in clinvar
(A;G) 0
(G;G) 0
ReferenceGRCh38 38.1/141
Chromosome5
Position35860966
GeneIL7R
is asnp
is mentioned by
dbSNPrs1494558
ebirs1494558
HLIrs1494558
Exacrs1494558
Varsomers1494558
Maprs1494558
PheGenIrs1494558
hapmaprs1494558
1000 genomesrs1494558
hgdprs1494558
ensemblrs1494558
gopubmedrs1494558
geneviewrs1494558
scholarrs1494558
googlers1494558
pharmgkbrs1494558
gwascentralrs1494558
openSNPrs1494558
23andMers1494558
23andMe allrs1494558
SNP Nexus

SNPshotrs1494558
SNPdbers1494558
MSV3drs1494558
GWAS Ctlgrs1494558
GMAF0.3871
Max Magnitude0

rs1494558, also known as Thr66Ile and Ile66Thr, is a variant in the IL7R interleukin 7 receptor gene. This SNP is unusual in being in "minus" orientation (relative to the reference genome). It is also a SNP in which the more common allele varies depending on the population; rs1494558(G) is generally more common in Caucasian populations, while rs1494558(A) is often more common in Asian populations. The (G) allele, on the minus strand, corresponds to the Thr codon, and the (A) allele corresponds to the Ile codon.

It is unclear if this SNP, either on it's own or together with rs1494555, is associated with risk for an autosomal recessive form (T-B+NK+) of severe combined immunodeficiency (SCID), as reported in both OMIM and ClinVar. An article published in 1998 ([PMID 9843216] described a single T-B+NK+ SCID patient shown by sequencing to carry rs1494558(A;A) and rs1494555(C;C) genotypes. This patient produced no IL7R mRNA (or protein), whereas his parents, who were both heterozygous at both SNPs, did and showed no SCID-associated phenotypes.

The authors conclude that this patient has a pair of defective IL7R alleles, however, "it remains to be determined if these amino acid changes are in fact disease-causing defects".[PMID 9843216] Given that neither SNP is particularly rare if enough populations are surveyed, whereas IL7R-deficient forms of SCID are quite rare (perhaps 1 in 500,000 births, based on CDC estimates), it seems quite likely that the causative mutation(s) leading to the defective IL7R alleles in the patient described in 1998 remain to be discovered and that they are not rs1494558 or rs1494555.

? (A;A) (A;G) (G;G) 28
OMIM146661
DescSEVERE COMBINED IMMUNODEFICIENCY, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE
Variant0001
Relatedalso


[PMID 22377791] Association of genetic polymorphisms of interleukins with new-onset diabetes after transplantation in renal transplantation


ClinVar
Risk rs1494558(G;G)
Alt rs1494558(G;G)
Reference rs1494558(A;A)
Significance Pathogenic
Disease Severe combined immunodeficiency not specified
Variation info
Gene IL7R
CLNDBN Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive not specified
Reversed 1
HGVS NC_000005.9:g.35861068T>C
CLNSRC OMIM Allelic Variant
CLNACC RCV000015964.25, RCV000121212.1,



[PMID 21326139] Prognostic significance of interleukin-7 receptor-alpha gene polymorphisms in allogeneic stem-cell transplantation: a confirmatory study.


GET Evidence
IL7R-I66T
aa_change Ile66Thr
aa_change_short I66T
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.698643
summary



[PMID 23692589OA-icon.png] Polymorphism in the interleukin-7 receptor-alpha and outcome after allogeneic hematopoietic cell transplantation with matched unrelated donor.