ATRIP p.Ala779=
c.2337G>A · rs201794728 · VCV774842
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.402%, sas)
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 -6.2 | GERP -2.9 |
| Overall | ||
| CADD | 0.999 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.402%
South Asian · 366/91,062 alleles
Filtering AF
0.368%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.355%
Overall
0.0344%
555/1,613,926 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.402% | 249 |
| Middle Eastern | 0.165% | 604 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,840 |
| European (non-Finnish) | 0.0126% | 7,919 |
| African / African-American | 0.00533% | 18,760 |
| Admixed American | 0.005% | 20,004 |
| East Asian | 0.00223% | 44,876 |
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
- ATRIP
- Protein
- p.Ala779=
- Coding
- c.2337G>A
- MANE Select
- NM_130384
- dbSNP
- rs201794728
- Type
- single nucleotide variant
- Location
- chr3:48465515 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
Similar variants
- ATRIP p.Ala779Val Uncertain significance ★★ ⚠ same residue
- ATRIP p.Ala779Ser Uncertain significance ★ ⚠ same residue
- ATRIP p.Ala779Thr Uncertain significance ★ ⚠ same residue
- TREX1 p.Arg114His Pathogenic/Likely pathogenic ★★ ⚠ same type
- TREX1 p.Arg164Ter Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Asp18Asn Pathogenic ★★ same type
- TREX1 p.Asp200His Likely pathogenic ★★ same type
- TREX1 p.Gln135Ter 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/atrip-p-ala779 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown