DGAT1 p.Arg404=
c.1212G>A · rs1554847189 · VCV2783786
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.057 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP 0.54 |
| Overall | ||
| CADD | 5.339 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,084 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.000411%
6/1,460,544 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00549% | 18,217 |
| East Asian | 0.00223% | 44,884 |
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.Arg404=
- Coding
- c.1212G>A
- MANE Select
- NM_012079
- dbSNP
- rs1554847189
- Type
- single nucleotide variant
- Location
- chr8:144317058 (GRCh38)
- Gene constraint
- LOEUF 1.055 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.86 · 5 PDB
- Residue 404
- the 'mboat fold' region; a binding site; 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-arg404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown