SPTA1 A970D

(SPTA1 Ala970Asp)

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This variant, also called alpha-IIa, has been seen frequently in individuals with recessive Hereditary spherocytosis. This appears to be the result of linkage to alpha-LEPRA (a C>T substitution at position -99 of intron 30); A970D is later reported as functionally neutral.

Variant evidence
Computational		-

Functional

Case/Control

Familial


Clinical importance
Severity		1

Treatability		4

Penetrance		-

Low clinical importance, Uncertain benign

(The "low clinical importance, uncertain" qualifier is assigned automatically based on the above evidence and importance scores.)

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Allele frequency

T @ chr1:158624528: 3.7% (370/9916) in EVS
T @ chr1:156891151: 1.6% (2/128) in GET-Evidence
Frequency shown in summary reports: 3.7% (370/9916)

Publications

They mention the allele α-LEPRA as also implicated in hereditary spherocytosis, a C>T substitution at position -99 of intron 30. They say this is linked in cis to the α-IIs (A970D) substitution. The α-LEPRA variant appears to be implicated as the causal variant.

This paper mentions A970D as a functionally neutral allele that is associated with α-LEPRA: “PCR screening of mutation αLEPRA and a functionally neutral mutation, Bughill (C→A, at position 11 of exon 21; GCT→GAT: A970D), which is inconstantly carried by allele αLEPRA”.

This variant is noted to be linked to alpha-LEPRA and is seen frequently in individuals with recessive Hereditary pyropoikilocytosis.

Genomes

Other external references

dbSNP

rs35948326
www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi

OMIM

Spherocytosis, type 3, autosomal recessive
www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=182860

Other in silico analyses

NBLOSUM100 score = 5
GET-Evidence autoscore = 3

Edit history

Nov 29 2012 Genome Importing Robot added CGI sample GS01669-DNA_D02 from PGP sample 27316983 view
Nov 29 2012 Genome Importing Robot added CGI sample GS01175-DNA_B04 from PGP sample 88590671 view
Mar 5 2012 Genome Importing Robot added hu232307 build 36 substitution variants view
Sep 20 2011 Madeleine Ball edited article 16150946 summary view
Sep 20 2011 Madeleine Ball edited article 15384986 summary view
Sep 20 2011 Madeleine Ball edited article 9067503 summary view
Sep 20 2011 Madeleine Ball edited article 8844207 summary view
Sep 20 2011 Madeleine Ball edited variant summary view
Sep 20 2011 Madeleine Ball edited article 9067503 summary view
Sep 20 2011 Madeleine Ball edited article 16150946 summary view
Sep 20 2011 Madeleine Ball edited article 15384986 summary view
Sep 20 2011 Madeleine Ball edited article 8844207 summary view
Sep 20 2011 Madeleine Ball edited variant summary view
Sep 20 2011 Madeleine Ball added article 9067503 view
Jun 23 2011 Genome Importing Robot removed James D. Watson view
Dec 5 2010 Genome Importing Robot added CGI sample GS00253-DNA_F01_200_37 view
May 10 2010 Madeleine Ball edited variant summary view
May 10 2010 Madeleine Ball edited variant summary view
May 10 2010 Madeleine Ball edited article 15384986 summary view
May 10 2010 Madeleine Ball edited article 8844207 summary view
May 10 2010 Madeleine Ball edited variant summary view
May 10 2010 Madeleine Ball added article 15384986 view
May 10 2010 Madeleine Ball edited article 16150946 summary view
May 10 2010 Madeleine Ball edited variant summary view
May 10 2010 Madeleine Ball edited article 8844207 summary view
May 10 2010 Madeleine Ball edited variant summary view
May 10 2010 Madeleine Ball added article 8844207 view
May 10 2010 Madeleine Ball removed article 3785322 view
May 10 2010 Madeleine Ball added article 3785322 view
May 8 2010 Genome Importing Robot added CGI sample GS00253-DNA_A02_200_37 view
Jan 13 2010 Abraham Rosenbaum edited article 16150946 summary view
Jan 13 2010 Abraham Rosenbaum edited variant summary view
Jan 13 2010 Abraham Rosenbaum added article 16150946 view
Jan 12 2010 Alexander Wait Zaranek edited variant summary view
Jan 5 2010 OMIM Importing Robot edited variant summary view
Dec 27 2009 Genome Importing Robot added James D. Watson view
Dec 27 2009 Genome Importing Robot added variant view

SPTA1 A970D - GET-Evidence