rs11006464 (FAM13C): De Novo Lipogenesis Variant
Key takeaways
- rs11006464 is located near FAM13C and the MRPL50P4 pseudogene on chromosome 10
- A CHARGE Consortium GWAS of 8,961 people studied this region for links to four fatty acids produced internally via de novo lipogenesis
- The alternate allele reduces FAM13C gene expression in testis tissue, based on GTEx data from 953 donors
- The same allele increases expression of a nearby gene (ENSG00000287969) in non-sun-exposed skin tissue
Key takeaways
- rs11006464 is located near FAM13C (Family With Sequence Similarity 13 Member C) and the MRPL50P4 pseudogene on chromosome 10
- A CHARGE Consortium genome-wide association study (GWAS) of 8,961 European-ancestry participants across five cohorts investigated this and related loci in relation to four fatty acids produced by the body through de novo lipogenesis (DNL)
- The alternate allele reduces FAM13C gene expression in testis tissue, based on GTEx v11 data from 953 donors
- The same allele increases expression of a nearby gene (ENSG00000287969) in non-sun-exposed suprapubic skin tissue
What the research says A GWAS conducted within the CHARGE Consortium enrolled 8,961 participants of European ancestry across five population-based cohorts to investigate common genetic variation in relation to plasma phospholipid levels of four fatty acids in the DNL pathway: palmitic acid (16:0), stearic acid (18:0), palmitoleic acid (16:1n-7), and oleic acid (18:1n-9). The study identified polymorphisms at seven novel loci associated with one or more of these fatty acids, spanning genes involved in protein glycosylation, polyunsaturated fatty acid metabolism, phospholipid remodeling, and glucose- and oxygen-sensing; specific association statistics for this locus are not detailed in the available study text. Tissue-specific eQTL analysis from GTEx v11 (953 donors, FDR<0.05) shows the alternate allele at this locus is linked to reduced FAM13C expression in testis and increased expression of ENSG00000287969 in non-sun-exposed suprapubic skin GTEx Portal.
Reported associations
- De novo lipogenesis pathway fatty acids (palmitic acid, stearic acid, palmitoleic acid, oleic acid): The CHARGE Consortium GWAS investigated genetic determinants of these four circulating fatty acids in 8,961 European-ancestry participants across five cohorts; this locus appears in this research context but specific effect sizes for rs11006464 are not available in the provided study excerpt
- FAM13C expression in testis: The alternate allele is associated with reduced FAM13C expression in testis tissue (eQTL slope -0.60, p=1.1e-5, 953 donors) GTEx Portal
- ENSG00000287969 expression in non-sun-exposed skin: The alternate allele is associated with increased expression in non-sun-exposed suprapubic skin (eQTL slope +0.60, p=1.7e-4, 953 donors) GTEx Portal
Evidence quality The CHARGE Consortium GWAS enrolled 8,961 European-ancestry participants across five population-based cohorts and applied genome-wide significance thresholds to identify seven novel loci, but the p-value and effect size specific to rs11006464 are not present in the available study text, making a precise assessment of evidence strength for the fatty acid association impossible at this time. The analysis was conducted exclusively in European-ancestry participants, limiting generalizability to other populations. The GTEx eQTL data are derived from 953 donors with FDR<0.05 correction applied within a cis-window, representing a controlled reference dataset; the eQTL associations at this locus (p=1.1e-5 in testis, p=1.7e-4 in skin) pass the significance threshold GTEx Portal. No independent replication of either the fatty acid GWAS finding or the eQTL signals is described in the available evidence.
Tissue-specific expression effects
- FAM13C: The alternate allele is associated with reduced expression in testis tissue GTEx Portal
- ENSG00000287969: The alternate allele is associated with increased expression in non-sun-exposed suprapubic skin GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is FAM13C and what does it do?
FAM13C (Family With Sequence Similarity 13 Member C) is a gene located on chromosome 10. Tissue expression data from GTEx show its activity varies by tissue, with carriers of the alternate allele at rs11006464 tending to show lower FAM13C activity specifically in testis.
What is de novo lipogenesis and why does rs11006464 appear in studies of it?
De novo lipogenesis (DNL) is the process by which the body converts carbohydrates and other nutrients into fatty acids, mainly in the liver. A large GWAS investigated genetic variants across the genome for links to four fatty acids produced this way, and the region containing rs11006464 appeared in that research context.
Is rs11006464 linked to heart disease or type 2 diabetes?
The study associated with this locus investigated circulating fatty acid levels, which have been linked to cardiometabolic conditions in prior research, but the available evidence does not directly associate rs11006464 with heart disease or diabetes.
What does an eQTL finding mean for rs11006464?
An expression quantitative trait locus (eQTL) means the variant influences how much of a nearby gene is produced in a specific tissue. For rs11006464, people carrying the alternate allele tend to show lower FAM13C gene output in testis tissue and higher output of a neighboring gene in skin, though the functional consequences of these differences are not yet established.