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NM_001098629.3(IRF5):c.*128T>C AND Systemic lupus erythematosus, association with susceptibility to, 10

Germline classification:
risk factor (1 submission)
Last evaluated:
Jul 1, 2007
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000003567.3

Allele description [Variation Report for NM_001098629.3(IRF5):c.*128T>C]

NM_001098629.3(IRF5):c.*128T>C

Gene:
IRF5:interferon regulatory factor 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q32.1
Genomic location:
Preferred name:
NM_001098629.3(IRF5):c.*128T>C
HGVS:
  • NC_000007.14:g.128948946T>C
  • NG_012306.1:g.16007T>C
  • NM_001098627.4:c.*128T>C
  • NM_001098629.3:c.*128T>CMANE SELECT
  • NM_001098630.3:c.*128T>C
  • NM_001242452.3:c.*128T>C
  • NM_001347928.2:c.*128T>C
  • NM_001364314.2:c.*128T>C
  • NM_032643.5:c.*128T>C
  • NC_000007.13:g.128589000T>C
  • NM_001098629.1:c.*128T>C
Nucleotide change:
C/T (rs2070197)
Links:
OMIM: 607218.0004; dbSNP: rs2070197
NCBI 1000 Genomes Browser:
rs2070197
Molecular consequence:
  • NM_001098627.4:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001098629.3:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001098630.3:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001242452.3:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001347928.2:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001364314.2:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_032643.5:c.*128T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Name:
Systemic lupus erythematosus, association with susceptibility to, 10
Identifiers:
MedGen: C4017076

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000023725OMIM
no assertion criteria provided
risk factor
(Jul 1, 2007) 		germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Genetic association of IRF5 with SLE in Mexicans: higher frequency of the risk haplotype and its homozygozity than Europeans.

Reddy MV, Velázquez-Cruz R, Baca V, Lima G, Granados J, Orozco L, Alarcón-Riquelme ME.

Hum Genet. 2007 Jul;121(6):721-7. Epub 2007 May 3.

PubMed [citation]
PMID:
17476532

Structural insertion/deletion variation in IRF5 is associated with a risk haplotype and defines the precise IRF5 isoforms expressed in systemic lupus erythematosus.

Kozyrev SV, Lewén S, Reddy PM, Pons-Estel B; Argentine Collaborative Group., Witte T; German Collaborative Group., Junker P, Laustrup H, Gutiérrez C, Suárez A, Francisca González-Escribano M, Martín J; Spanish Collaborative Group., Alarcón-Riquelme ME.

Arthritis Rheum. 2007 Apr;56(4):1234-41.

PubMed [citation]
PMID:
17393452
See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000023725.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a case-control study of IRF5 SNPs in Mexican patients with SLE (SLEB10; 612251), Reddy et al. (2007) found a significant disease association with 3 different SNPs in the IRF5 gene. The strongest association was for allele C of rs2070197, which tagged a risk haplotype (combined case-control analysis, P = 1.26 x 10(-21)). The frequency of this risk haplotype was significantly higher in healthy Mexican individuals, and even higher in healthy Mexican Indians, compared to healthy individuals of European ancestry. The C allele of rs2070197 is a tag for a risk haplotype and is itself not functional; Kozyrev et al. (2007) found that this SNP broke up the originally identified haplotype (Graham et al., 2006; Cunninghame Graham et al., 2007) into an ancestral haplotype of lower frequency that contained additional risk alleles. Carriers of the risk haplotype tagged by C allele of rs2070197 express alternative IRF5 protein isoforms and have high levels of IRF5 mRNA and transcripts from the alternative exon 1B.

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

Last Updated: Dec 24, 2023