rs560426
This variant is located in the ABCA4 gene.
▶GWAS Catalog Trait Associations (1)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
GWAS Catalog Trait Associations (1)
Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.
orofacial cleft
▶Research that mentions this SNP (5)
▶Interactions between superoxide dismutase and paraoxonase polymorphic variants in nonsyndromic cleft lip with or without cleft palate in the Brazilian populationAssociationN=1,915Renato Assis Machado et al.(2019)· Environmental and Molecular Mutagenesis
Two-stage genetic study examining 28 SNPs in oxidative stress genes (SOD1, SOD2, SOD3, PON1, PON2, PON3) in relation to nonsyndromic cleft lip with or without cleft palate (NSCL/CP) in Brazilian population. Initial transmission disequilibrium test (TDT) on 325 trios identified gene-gene interactions, which were validated in case-control analysis (722 cases, 866 controls). PON1 rs2237583 C allele showed protective effect (OR=0.79, 95% CI 0.67-0.93, p=0.005), and multiple significant PON1-PON2-PON3 gene-gene interactions were detected after Bonferroni correction.
▶Genetic risk factors for orofacial clefts in Central Africans and Southeast AsiansAssociationN=993Jane C. Figueiredo et al.(2014)· American Journal of Medical Genetics Part A
A targeted genome-wide study examining SNPs in three understudied populations (260 children with orofacial clefts from the DRC, Vietnam, and Philippines) confirmed four cleft susceptibility regions: 1q32.2 (IRF6), 10q25.3 (VAX1), 17q22 (NOG), and 15q13.3. Notable findings include rs10787738 near VAX1 (P=4.98E-03) and rs7987165 on chromosome 13 (P=2.2E-05) in meta-analysis, with risk alleles varying by population and no significant associations found in African populations.
▶Association between single‐nucleotide polymorphisms on chromosome 1p22 and 20q12 and nonsyndromic cleft lip with or without cleft palate: New data in Han Chinese and meta‐analysisMeta-analysisN=2,087Enmin Huang et al.(2012)· Birth Defects Research Part A: Clinical and Molecular Teratology
This replication and meta-analysis study confirmed that SNPs on chromosome 20q12 (rs6072081, rs13041247, rs6102085) are significantly associated with reduced risk of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Han Chinese populations, with protective effects (OR 0.62-0.72). However, rs560426 on chromosome 1p22 showed inconsistent associations across populations. A meta-analysis of 676 cases and 740 controls found rs13041247 C allele strongly protective (pooled OR 0.63, 95% CI 0.57-0.69) while rs560426 showed only marginal increased risk (pooled OR 1.23, 95% CI 1.04-1.47, p=0.02).
▶Different roles of two novel susceptibility loci for nonsyndromic orofacial clefts in a Chinese Han population.AssociationN=780Yongchu Pan et al.(2011)· American Journal of Medical Genetics Part A
This case-control study of 396 nonsyndromic orofacial cleft cases and 384 controls in a Chinese Han population confirms that rs13041247 near MAFB is associated with decreased NSOC risk (C allele frequency 0.497 in controls vs 0.356 in cases), with protective effects observed across cleft lip phenotypes. The rs560426 variant near ABCA4 showed no significant association with NSOC in this population, demonstrating population-specific effects of previously identified GWAS loci.
▶Association of common variants, not rare mutations, in IRF6 With nonsyndromic clefts in a honduran populationAssociationN=352Yuna C. Larrabee et al.(2011)· The Laryngoscope
This family-based association study examined the correlation between IRF6 rs642961 polymorphism and nonsyndromic cleft lip with or without cleft palate (NSCL/P) in 352 Iranian individuals from 102 nuclear families. Using FBAT statistical analysis, the study found no significant association between the rs642961 variant and NSCL/P risk under additive (p=0.76), dominant (p=0.66), or recessive (p=0.9) genetic models, contrasting with previous findings in other populations and suggesting population-specific genetic effects.
About ABCA4
The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]
View all ABCA4 variants →Gene information from NCBI Gene. Variant classifications from ClinVar.
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