SMOC2
short-face candidate
SMOC2 chr1:56.4Mb (Marchant 2017). Top brachycephaly hit in our village-baseline selection scan at |dP|=0.85. The H1 hardening test (logistic regression of brachy phenotype on the rep SNP) showed R^2=0.05 alone, vs R^2=0.96 with a genome-wide PRS - the rep SNP is necessary-but-not-sufficient.
short-face allele common at this rep SNP - BUT brachy is polygenic and SMOC2 alone does not cleanly tag the phenotype (some non-brachy breeds also read high here, e.g. Afghan Hound, Cardigan Welsh Corgi)
long-face allele common - this direction reliably distinguishes non-brachy from brachy/intermediate (Bull Terrier, Leonberger, Newfoundland, Saint Bernard read at the bottom)
- 100% n=21
- 100% n=14
- 100% n=102
- 100% n=8
- 100% n=26
- 100% n=96
- 100% n=24
- 100% n=31
- 100% n=33
- 100% n=38
- 0% n=10
- 2% n=25
- 2% n=44
- 12% n=182
- 13% n=37
- 17% n=23
- 20% n=40
- 20% n=10
- 22% n=192
- 25% n=16
Frequency is measured at the typed-backbone 1:56398416 on chr1, 56.4 Mb (inside the gene body). Alleles A/G. Coordinates from ensembl symbol UU Cfam GSD 1.0. Per-breed frequencies are computed across all CanVAS dogs labelled with that breed (missing genotypes excluded). See methodology for the full pipeline.