DGAT2 p.Pro380=
c.1140G>A · VCV4683660
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -5.5 | GERP -3.9 |
| Overall | ||
| CADD | 3.267 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0026%
Overall
0.00366%
59/1,614,058 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| South Asian | 0.00769% | 13,007 |
| Admixed American | 0.005% | 20,003 |
| European (non-Finnish) | 0.00381% | 26,222 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,252 |
| African / African-American | 0.00133% | 75,040 |
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
- DGAT2
- Protein
- p.Pro380=
- Coding
- c.1140G>A
- MANE Select
- NM_032564
- Type
- single nucleotide variant
- Location
- chr11:75800481 (GRCh38)
- Gene constraint
- LOEUF 0.93 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.52
Similar variants
- DGAT2 p.Pro380Gln Uncertain significance ★ ⚠ same residue
- DGAT2 p.Pro380Leu Uncertain significance ★ ⚠ same residue
- DGAT2 p.Glu15Val Uncertain significance ★★ ⚠ same type
- DGAT2 p.Ile313Val Uncertain significance ★★ ⚠ same type
- DGAT2 p.Tyr223Ser Uncertain significance ★★ ⚠ same type
- DGAT2 p.Arg297Gln Benign/Likely benign ★★ ⚠ same type
- DGAT2 p.Gly318Ser Likely benign ★★ ⚠ same type
- DGAT2 p.Ile355= Likely benign ★★ 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/dgat2-p-pro380 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown