DGAT1 p.Asp475=
c.1425C>T · rs1031073510 · VCV2092479
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.5e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.4 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 7.625 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.5e-05%
European (non-Finnish) · 1/1,176,662 alleles
Overall
6.88e-05%
1/1,453,268 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DGAT1
- Protein
- p.Asp475=
- Coding
- c.1425C>T
- MANE Select
- NM_012079
- dbSNP
- rs1031073510
- Type
- single nucleotide variant
- Location
- chr8:144316596 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.86 · 5 PDB
- Residue 475
- the 'mboat fold' region; a UniProt-annotated variant site (in diar7; uncertain significance); an α-helix
Similar variants
- DGAT1 c.1094+2T>C Pathogenic/Likely pathogenic ★★ same type
- DGAT1 c.1160+1G>A Likely pathogenic ★★ same type
- DGAT1 c.574+1G>T Likely pathogenic ★★ same type
- DGAT1 c.676+1G>A Likely pathogenic ★★ same type
- DGAT1 c.751+2T>C Pathogenic ★★ same type
- DGAT1 p.Arg280Ter Pathogenic/Likely pathogenic ★★ same type
- DGAT1 p.Arg395Ter Pathogenic/Likely pathogenic ★★ same type
- DGAT1 p.Gln119Ter Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dgat1-p-asp475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown