ATRIP p.Thr691=
c.2073G>A · rs372328016 · VCV2884412
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.39 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.2 |
| Overall | ||
| CADD | 0.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,900 alleles
Filtering AF
0.00224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00261%
42/1,612,136 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,967 |
| South Asian | 0.0033% | 30,339 |
| European (non-Finnish) | 0.00305% | 32,741 |
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.Thr691=
- Coding
- c.2073G>A
- MANE Select
- NM_130384
- dbSNP
- rs372328016
- Type
- single nucleotide variant
- Location
- chr3:48464848 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
Similar variants
- ATRIP p.Thr691Met 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
- 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-thr691 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown