ATRIP p.Ser154=
c.462C>T · rs752036149 · VCV2176489
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0101%, nfe)
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 -2.5 | GERP -3.6 |
| Overall | ||
| CADD | 9.717 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0101%
European (non-Finnish) · 119/1,179,072 alleles
Filtering AF
0.0086%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00804%
Overall
0.00775%
125/1,612,434 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0101% | 9,908 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,481 |
| African / African-American | 0.00134% | 74,900 |
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.Ser154=
- Coding
- c.462C>T
- MANE Select
- NM_130384
- dbSNP
- rs752036149
- Type
- single nucleotide variant
- Location
- chr3:48451809 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
- Residue 154
- the 'interaction with cinp' region
Similar variants
- TREX1 p.Asp154= Benign/Likely benign ★★ same residue
- TREX1 p.Asp154Ala Likely pathogenic ★ same residue
- ATRIP p.Ser154Cys Uncertain significance ★ ⚠ same residue
- ATRIP p.Ser154Tyr 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
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-ser154 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown