NM_080424.2(SP110):c.752-483C>T AND Mycobacterium tuberculosis, susceptibility to

Clinical significance:Uncertain significance (Last evaluated: Apr 1, 2007)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000005878.5

Allele description [Variation Report for NM_080424.2(SP110):c.752-483C>T]

NM_080424.2(SP110):c.752-483C>T

Genes:
SP110:SP110 nuclear body protein [Gene - OMIM - HGNC]
SP140:SP140 nuclear body protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q37.1
Genomic location:
Preferred name:
NM_080424.2(SP110):c.752-483C>T
HGVS:
  • NC_000002.12:g.230210491G>A
  • NG_008295.1:g.14622C>T
  • NM_080424.2:c.752-483C>T
  • LRG_109t1:c.752-483C>T
  • LRG_109:g.14622C>T
  • NC_000002.11:g.231075206G>A
Nucleotide change:
C-T, INTRON 6 (rs2114592)
Links:
OMIM: 604457.0004; dbSNP: rs2114592
NCBI 1000 Genomes Browser:
rs2114592
Molecular consequence:
  • NM_080424.2:c.752-483C>T - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Mycobacterium tuberculosis, susceptibility to
Identifiers:
MedGen: C1834752; OMIM: 607948

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000026060OMIMno assertion criteria providedUncertain significance
(Apr 1, 2007)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Variants in the SP110 gene are associated with genetic susceptibility to tuberculosis in West Africa.

Tosh K, Campbell SJ, Fielding K, Sillah J, Bah B, Gustafson P, Manneh K, Lisse I, Sirugo G, Bennett S, Aaby P, McAdam KPWJ, Bah-Sow O, Lienhardt C, Kramnik I, Hill AVS.

Proc Natl Acad Sci U S A. 2006 Jul 5;103(27):10364-10368. doi: 10.1073/pnas.0603340103. Epub 2006 Jun 27.

PubMed [citation]
PMID:
16803959
PMCID:
PMC1502463

No associations of human pulmonary tuberculosis with Sp110 variants.

Thye T, Browne EN, Chinbuah MA, Gyapong J, Osei I, Owusu-Dabo E, Niemann S, RĂ¼sch-Gerdes S, Horstmann RD, Meyer CG.

J Med Genet. 2006 Jul;43(7):e32.

PubMed [citation]
PMID:
16816019
PMCID:
PMC2564561
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000026060.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

This variant, formerly titled MYCOBACTERIUM TUBERCULOSIS, SUSCEPTIBILITY TO (see 607948), has been reclassified based on the findings of Thye et al. (2006) and Szeszko et al. (2007).

Tosh et al. (2006) examined 27 SNPs in the SP110 gene in 219 Gambian families and identified 3 that were associated with tuberculosis, including T/C in intron 6 (rs2114592). The most common allele (T) was transmitted more often than expected to affected offspring. Examination of an additional 99 Guinean and 102 Guinea-Bissau families independently replicated the association. The SNP did not affect a known functional domain of SP110.

Thye et al. (2006) observed no significant differences in the frequencies of 21 SP110 variants, including leu425 to ser (604457.0003), between 2,004 sputum-positive, HIV-negative Ghanaian tuberculosis patients and 1,231 exposed, healthy personal contacts and 1,135 community controls. They concluded that an association of SP110 variants and distinct phenotypes of human M. tuberculosis infection is doubtful.

Szeszko et al. (2007) genotyped 29 SNPs in SP110, including 7 causing amino acid changes, and 15 ancestry-informative markers as genomic controls in nearly 2,000 HIV-seronegative, M. tuberculosis culture-positive Russians and a similar number of controls. They found no evidence for association of SP11O SNPs, including leu425 to ser, with susceptibility to adult pulmonary tuberculosis. Szeszko et al. (2007) proposed that the effect of SP110 polymorphisms in outbred human populations may be smaller than the effect of Ipr1 in inbred mice and emphasized the importance of whole-genome scans to identify genes and causal variants predisposing to tuberculosis in human populations.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 30, 2019

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