rs642961

A SNP on chromosome 1. Its most notable genotype is A;A: 2.40x increased risk of cleft lip

Gene
None listed
Location
Chr 1209,815,925 (GRCh38)
Highest magnitude
2.0Worth knowing
Tested on
23andMe, AncestryDNA
Minor allele frequency
17%

Genotypes

As shown in 23andMe and AncestryDNA files.

  1. A;AMost notableBad2.40x increased risk of cleft lipWorth knowing · 2.03% of people
  2. A;GBad1.68x increased risk of cleft lipMinor · 1.527% of people
  3. G;GGoodNormal risk of cleft lipMinor · 1.071% of people

On SNPedia: (A;A), (A;G), (G;G). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Frequency

Share of each genotype in 11 HapMap populations.

  • AverageA;A 3% A;G 27% G;G 71%
  • European ancestry (Utah)A;A 5% A;G 34% G;G 61%
  • Han Chinese (Beijing)A;A 3% A;G 30% G;G 67%
  • Japanese (Tokyo)A;A 3% A;G 30% G;G 68%
  • Yoruba (Nigeria)A;A 1% A;G 16% G;G 82%
  • African ancestry (Southwest US)A;A 0% A;G 18% G;G 83%
  • Chinese (Denver)A;A 7% A;G 26% G;G 68%
  • Gujarati IndianA;A 5% A;G 38% G;G 57%
  • Luhya (Kenya)A;A 0% A;G 13% G;G 87%
  • Mexican ancestry (Los Angeles)A;A 2% A;G 37% G;G 61%
  • Maasai (Kenya)A;A <1% A;G 16% G;G 83%
  • TuscanA;A 5% A;G 36% G;G 59%

Notes

From SNPedia

Show notes, about 260 words

risk of cleft lip 23andMe considers rs861020 a proxy Associated with European Facial Appearance *rs7590268 *rs16903544 *rs987525 *rs9574565 *rs227731 *rs642961 *rs1258763 Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Lack of association between IRF6 polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Current concepts in genetics of nonsyndromic clefts. Studies of palatine rugae and interferon regulatory factor 6 variations in a group of families with sporadic hypodontia. IRF6 gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Family-based study shows heterogeneity of a susceptibility locus on chromosome 8q24 for nonsyndromic cleft lip and palate. Association between genetic variants of reported candidate genes or regions and risk of cleft lip with or without cleft palate in the polish population. IRF6 polymorphisms are associated with nonsyndromic orofacial clefts in a Chinese Han population. Single-nucleotide polymorphisms (SNPs) of the IRF6 and TFAP2A in non-syndromic cleft lip with or without cleft palate (NSCLP) in a northern Chinese population. Association of common variants, not rare mutations, in IRF6 with nonsyndromic clefts in a Honduran population. MCS9.7 enhancer activity is highly, but not completely, associated with expression of Irf6 and p63. Cleft Lip and Cleft Palate

Source and license

Adapted from rs642961 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.