ATRIP p.Glu134del
c.395AAG[2] · rs781110153 · VCV2984331
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.009%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 20.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.009%
East Asian · 4/44,454 alleles
Filtering AF
0.00302%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0027%
Overall
0.00365%
58/1,589,140 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.009% | 11,113 |
| Remaining individualsnot grpmax-eligible | 0.00651% | 15,362 |
| European (non-Finnish) | 0.00394% | 25,392 |
| African / African-American | 0.00271% | 36,944 |
| South Asian | 0.00232% | 43,062 |
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.Glu134del
- Coding
- c.395AAG[2]
- MANE Select
- NM_130384
- dbSNP
- rs781110153
- Type
- Microsatellite
- Location
- chr3:48451741 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
- Residue 134
- the 'interaction with cinp' region
Similar variants
- TREX1 p.Leu134Phe Uncertain significance ★★ ⚠ same residue
- TREX1 p.Leu134fs Pathogenic ★ same residue
- ATRIP p.Glu134Asp Uncertain significance ★ ⚠ same residue
- ATRIP p.Glu134Val Uncertain significance ★ ⚠ same residue
- TREX1 p.Leu134Ile Uncertain significance ★ ⚠ same residue
- TREX1 p.Ala72fs Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Gln51fs Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Ser82fs 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-glu134del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown