SP110 L425S - GET-Evidence

Curation:

(See latest approved version)
Currentness:

SP110 L425S

(SP110 Leu425Ser)


Short summary

This variant is associated with a slightly increased risk of tuberculosis. It is unclear whether it is itself causal, or in linkage disequilibrium with some other causal variant that has a stronger effect.

Variant evidence
Computational

Disruptive amino acid change (BLOSUM100 = 4), but not a conserved region.

See Tosh K et al. 2006 (16803959).

Functional -
Case/Control 4

p = 0.01

See Tosh K et al. 2006 (16803959).

Familial
 
Clinical importance
Severity 4

High mortality rate for infected individuals

Treatability 4

Treatment is difficult, often requiring multiple antibiotics

Penetrance 1

Slightly increased risk

 

Impact

Low clinical importance, Uncertain pathogenic

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

Inheritance pattern

undefined

Summary of published research, and additional commentary

 

Allele frequency

  • G @ chr2:231050715: 86.3% (9288/10758) in EVS
  • G @ chr2:230758958: 89.1% (114/128) in GET-Evidence
  • Frequency shown in summary reports: 86.3% (9288/10758)

Publications
 

Tosh K, Campbell SJ, Fielding K, Sillah J, Bah B, Gustafson P, Manneh K, Lisse I, Sirugo G, Bennett S, Aaby P, McAdam KP, Bah-Sow O, Lienhardt C, Kramnik I, Hill AV. Variants in the SP110 gene are associated with genetic susceptibility to tuberculosis in West Africa. Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10364-8. Epub 2006 Jun 27. PubMed PMID: 16803959; PubMed Central PMCID: PMC1502463.

This variant is associated with susceptibility to tuberculosis in West Africans (Gambian, Guinean, and Guinea-Bissau), p = 0.01. 347 alleles were found in affected children, 335 were expected.

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
hom G @ chr2:231050715

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
hom G @ chr2:231050715

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
hom G @ chr2:231050715

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom G @ chr2:231050715

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het G @ chr2:231050715

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
hom G @ chr2:231050715

 

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom G @ chr2:231050715

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom G @ chr2:231050715

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
hom G @ chr2:231050715

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom G @ chr2:231050715

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
hom G @ chr2:231050715

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom G @ chr2:231050715

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het G @ chr2:231050715

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
hom G @ chr2:231050715

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
hom G @ chr2:231050715

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het G @ chr2:231050715

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
hom G @ chr2:231050715

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
hom G @ chr2:231050715

 

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom G @ chr2:231050715

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het G @ chr2:231050715

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het G @ chr2:231050715

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
hom G @ chr2:231050715

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom G @ chr2:231050715

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het G @ chr2:231050715

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom G @ chr2:231050715

 

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
hom G @ chr2:231050715

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
hom G @ chr2:231050715

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het G @ chr2:231050715

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
hom G @ chr2:231050715

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het G @ chr2:231050715

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom G @ chr2:231050715

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
hom G @ chr2:231050715

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
hom G @ chr2:231050715

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom G @ chr2:231050715

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom G @ chr2:231050715

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het G @ chr2:231050715

 

GS06985 - var-GS06985-1100-36-ASM
hom G @ chr2:230758959

 

GS06994 - var-GS06994-1100-36-ASM
hom G @ chr2:230758959

 

GS07357 - var-GS07357-1100-36-ASM
hom G @ chr2:230758959

 

GS10851 - var-GS10851-1100-36-ASM
hom G @ chr2:230758959

 

GS12004 - var-GS12004-1100-36-ASM
het G @ chr2:230758959

 

GS18501 - var-GS18501-1100-36-ASM
hom G @ chr2:230758959

 

GS18502 - var-GS18502-1100-36-ASM
hom G @ chr2:230758959

 

GS18504 - var-GS18504-1100-36-ASM
hom G @ chr2:230758959

 

GS18505 - var-GS18505-1100-36-ASM
hom G @ chr2:230758959

 

GS18508 - var-GS18508-1100-36-ASM
hom G @ chr2:230758959

 

GS18517 - var-GS18517-1100-36-ASM
hom G @ chr2:230758959

 

GS18526 - var-GS18526-1100-36-ASM
hom G @ chr2:230758959

 

GS18537 - var-GS18537-1100-36-ASM
hom G @ chr2:230758959

 

GS18555 - var-GS18555-1100-36-ASM
hom G @ chr2:230758959

 

GS18558 - var-GS18558-1100-36-ASM
hom G @ chr2:230758959

 

GS18940 - var-GS18940-1100-36-ASM
hom G @ chr2:230758959

 

GS18942 - var-GS18942-1100-36-ASM
hom G @ chr2:230758959

 

GS18947 - var-GS18947-1100-36-ASM
hom G @ chr2:230758959

 

GS18956 - var-GS18956-1100-36-ASM
hom G @ chr2:230758959

 

GS19017 - var-GS19017-1100-36-ASM
hom G @ chr2:230758959

 

GS19020 - var-GS19020-1100-36-ASM
hom G @ chr2:230758959

 

GS19025 - var-GS19025-1100-36-ASM
hom G @ chr2:230758959

 

GS19026 - var-GS19026-1100-36-ASM
hom G @ chr2:230758959

 

GS19129 - var-GS19129-1100-36-ASM
hom G @ chr2:230758959

 

GS19238 - var-GS19238-1100-36-ASM
het G @ chr2:230758959

 

GS19239 - var-GS19239-1100-36-ASM
hom G @ chr2:230758959

 

GS19240 - var-GS19240-1100-36-ASM
hom G @ chr2:230758959

 

GS19648 - var-GS19648-1100-36-ASM
hom G @ chr2:230758959

 

GS19649 - var-GS19649-1100-36-ASM
hom G @ chr2:230758959

 

GS19669 - var-GS19669-1100-36-ASM
hom G @ chr2:230758959

 

GS19670 - var-GS19670-1100-36-ASM
hom G @ chr2:230758959

 

GS19700 - var-GS19700-1100-36-ASM
het G @ chr2:230758959

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr2:230758959

 

GS19703 - var-GS19703-1100-36-ASM
hom G @ chr2:230758959

 

GS19704 - var-GS19704-1100-36-ASM
hom G @ chr2:230758959

 

GS19735 - var-GS19735-1100-36-ASM
hom G @ chr2:230758959

 

GS19834 - var-GS19834-1100-36-ASM
hom G @ chr2:230758959

 

GS20502 - var-GS20502-1100-36-ASM
hom G @ chr2:230758959

 

GS20509 - var-GS20509-1100-36-ASM
hom G @ chr2:230758959

 

GS21767 - var-GS21767-1100-36-ASM
hom G @ chr2:230758959

 

Other external references
 

    dbSNP
  • rs3948464
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the SP110 gene
    Hepatic Veno-occlusive Disease with Immunodeficiency
    Charcot-Marie-Tooth Neuropathy Type 1
    Charcot-Marie-Tooth Neuropathy Type 1A
    Charcot-Marie-Tooth Neuropathy Type 1E
    Hereditary Neuropathy with Liability to Pressure Palsies
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SP110
    Web search results (31 hits -- see all)

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 4

Edit history
 

Gene search

"GENE" or "GENE A123C":

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