ATRIP p.Thr265=
c.795G>A · rs779664499 · VCV1932595
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00686%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.32 | loss · gain 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.37 | GERP -0.38, phastCons 0.001 |
| Overall | ||
| CADD | 8.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00686%
South Asian · 6/87,524 alleles
Filtering AF
0.00296%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00201%
Overall
0.0015%
24/1,596,142 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00686% | 14,587 |
| Admixed American | 0.00348% | 28,723 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,839 |
| Finnishnot grpmax-eligible | 0.00157% | 63,720 |
| African / African-American | 0.00135% | 73,916 |
| European (non-Finnish) | 0.00102% | 97,666 |
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.Thr265=
- Coding
- c.795G>A
- MANE Select
- NM_130384
- dbSNP
- rs779664499
- Type
- single nucleotide variant
- Location
- chr3:48457382 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
Similar variants
- ATRIP p.Thr265Met Uncertain significance ★★ ⚠ same residue
- TREX1 p.Gly265= Likely benign ★ 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
- ATRIP p.Ala119Thr Uncertain significance ★★ ⚠ 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-thr265 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown