rs13041247

This is a intergenic variant variant in the LOC102724968 gene.

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GWAS Catalog Trait Associations (2)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

Cleft palate, cleft lip

Sun Y et al. “Genome-wide association study identifies a new susceptibility locus for cleft lip with or without a cleft palate.” Nature Communications 6:6414 (2015)
Allele T
OR 1.32
p 2.0e-11
N 2,106
Large GWAS
East Asian

orofacial cleft

Ludwig KU et al. “Genome-wide meta-analyses of nonsyndromic cleft lip with or without cleft palate identify six new risk loci.” Nature Genetics 44(9):968-71 (2012)
Allele T
OR 1.19
p 6.0e-9
N 2,383
Large GWAS
multi-ancestry
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Research that mentions this SNP (3)

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Genetic risk factors for orofacial clefts in Central Africans and Southeast Asians
AssociationN=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.

Traits studied:Cleft lip with or without cleft palateNon-syndromic cleft lipNon-syndromic cleft palateOrofacial clefts
PubMedDOIMetascience Observatory
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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‐analysis
Meta-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).

Traits studied:Nonsyndromic cleft lip only (NSCLO)Nonsyndromic cleft lip with cleft palate (NSCLP)Nonsyndromic cleft lip with or without cleft palate (NSCL/P)
PubMedDOIMetascience Observatory
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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.

Traits studied:Cleft lip only (CLO)Cleft lip with cleft palate (CLP)Cleft lip with or without cleft palate (CL/P)Cleft palate only (CPO)Nonsyndromic orofacial clefts
PubMedDOIMetascience Observatory

This variant is in our database but has no known associations or PRS memberships yet.

Gene information from NCBI Gene. Variant classifications from ClinVar.

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