DGAT1 p.Asp313=
c.939C>T · rs1300887097 · VCV2830973
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.84 | GERP -3.6 |
| Overall | ||
| CADD | 3.353 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,032 alleles
Overall
0.000657%
1/152,176 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.Asp313=
- Coding
- c.939C>T
- MANE Select
- NM_012079
- dbSNP
- rs1300887097
- Type
- single nucleotide variant
- Location
- chr8:144317586 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.86 · 5 PDB
- Residue 313
- the 'mboat fold' region; a turn
Similar variants
- DGAT1 p.Asp313Asn Uncertain significance ★ ⚠ same residue
- 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
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-asp313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown