SPTA1 A970D - GET-Evidence


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(SPTA1 Ala970Asp)

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Short summary

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

Polyphen 2 unknown

Functional 1

Reported to be functionally neutral?

See Tse WT et al. 1997 (9067503).



Familial -
Clinical importance
Severity -
Treatability -
Penetrance -


Low clinical importance, Uncertain benign

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

Inheritance pattern


Summary of published research, and additional commentary


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)


Maillet P, Alloisio N, Morlé L, Delaunay J. Spectrin mutations in hereditary elliptocytosis and hereditary spherocytosis. Hum Mutat. 1996;8(2):97-107. PubMed PMID: 8844207.

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.

Tse WT, Gallagher PG, Jenkins PB, Wang Y, Benoit L, Speicher D, Winkelmann JC, Agre P, Forget BG, Marchesi SL. Amino-acid substitution in alpha-spectrin commonly coinherited with nondominant hereditary spherocytosis. Am J Hematol. 1997 Mar;54(3):233-41. PubMed PMID: 9067503.

Mentions finding of the A970D variant and concludes it is in linkage disequilibrium with another causal variant.

Delaunay J, Nouyrigat V, Proust A, Schischmanoff PO, Cynober T, Yvart J, Gaillard C, Danos O, Tchernia G. Different impacts of alleles alphaLEPRA and alphaLELY as assessed versus a novel, virtually null allele of the SPTA1 gene in trans. Br J Haematol. 2004 Oct;127(1):118-22. PubMed PMID: 15384986.

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”.

Costa DB, Lozovatsky L, Gallagher PG, Forget BG. A novel splicing mutation of the alpha-spectrin gene in the original hereditary pyropoikilocytosis kindred. Blood. 2005 Dec 15;106(13):4367-9. Epub 2005 Sep 8. PubMed PMID: 16150946; PubMed Central PMCID: PMC1895230.

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


hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr1:158624528


hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het T @ chr1:158624528



Added in this revision:

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het T @ chr1:158624528


Other external references

  • rs35948326

Other in silico analyses

  • NBLOSUM100 score = 5
  • GET-Evidence autoscore = 3

Edit history

Gene search

"GENE" or "GENE A123C":

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