ATRIP p.Pro280Thr
c.838C>A · VCV3976087
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely benign
0.0478 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
0/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0478 | likely benign |
|---|---|---|
| REVEL | 0.01 | strongly benign-leaning |
| SaProt | LLR -6.79 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.96 | GERP 0.48, phastCons 0.02 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 19 kb · p 0.089 · regional, not allelic |
| Overall | ||
| CADD | 0.692 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ATRIP
- Protein
- p.Pro280Thr
- Coding
- c.838C>A
- MANE Select
- NM_130384
- Type
- single nucleotide variant
- Location
- chr3:48459367 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
Similar variants
- ATRIP p.Pro280= 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
- ATRIP p.Ala173Val 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-pro280thr (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown