rs10496410 (PPP1R2P5/LINC01789): Cleft Lip GWAS

Key takeaways

• rs10496410 is located near PPP1R2P5 (a pseudogene) and LINC01789 (a long non-coding RNA), two genomic elements with limited published characterization
• This variant was included in a genome-wide scan of more than 1,900 families affected by cleft lip with or without cleft palate (CL/P)
• The study examined whether genetic variants interact with maternal smoking, alcohol use, or vitamin supplementation during early pregnancy
• No specific effect size or significance threshold for rs10496410 is reported in the available study text
• Any association between this variant and CL/P or other traits should be treated as unconfirmed

What the research says The single source covering this locus is a genome-wide scan of 1,908 nuclear families (5,424 individuals total) affected by isolated CL/P - a common orofacial birth defect affecting roughly 3.4 to 22.9 per 10,000 live births - drawn from European (n=825), Asian (n=1,024), and other (n=59) ancestry groups and screened across 341,191 SNPs after quality control. The study applied a parent-of-origin (PoO) methodology - a framework testing whether a variant's effect differs when inherited from the mother versus the father - against three periconceptional exposures: maternal cigarette smoking, alcohol consumption, and vitamin supplementation. The study's reported highlights centered on ANK3 variants interacting with maternal smoking and ARHGEF10 variants interacting with alcohol in European families; no results specific to rs10496410 or this locus are described in the available text.

Reported associations

• Cleft lip with or without cleft palate (CL/P): rs10496410 falls within the genomic region analyzed in this CL/P triad GWAS; however, no association result, p-value, or effect size for this variant is provided in the available study excerpts

Evidence quality The sole available source is a 2020 genome-wide study conducted on 1,908 case-parent triads and dyads for isolated CL/P. The study screened 341,191 SNPs after quality control and applied parent-of-origin interaction tests against maternal smoking, alcohol use, and vitamin supplementation across European, Asian, and pooled samples. The study's primary reported hits were ANK3 (p=2.6×10^-6 for PoO×Smoking in Europeans) and ARHGEF10 (p=2.9×10^-6 for PoO×Alcohol in Europeans), which the authors themselves described as requiring independent replication. No p-value, q-value, or effect size for rs10496410 appears in the provided text; the evidence quality for this specific variant therefore cannot be assessed.

Lifestyle considerations No lifestyle considerations on file for this variant.