ATRIP p.Pro16=
c.48G>A · VCV3976968
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0224%, 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 0.48 | GERP -3.2, phastCons 0.001 |
| Overall | ||
| CADD | 8.699 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0224%
South Asian · 12/53,492 alleles
Filtering AF
0.0129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0101%
Overall
0.00177%
22/1,241,354 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0224% | 4,458 |
| European (non-Finnish) | 0.000928% | 107,709 |
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.Pro16=
- Coding
- c.48G>A
- MANE Select
- NM_130384
- Type
- single nucleotide variant
- Location
- chr3:48446893 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
- Residue 16
- the 'disordered' region
Similar variants
- ATRIP p.Pro16Leu 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-pro16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown