ALPI p.Pro94Ser
c.280C>T · VCV3288298
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.3542 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
REVEL, SaProt · AlphaMissense no call
Computational evidence
| Protein change | ||
| AlphaMissense | 0.3542 | ambiguous |
|---|---|---|
| REVEL | 0.918 | moderately pathogenic-leaning |
| SaProt | LLR -8.56 | tolerated |
| ⇒ REVEL calls this damaging; SaProt does not; AlphaMissense makes no call. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 2,943 bp · p 0.26 · regional, not allelic |
| Overall | ||
| CADD | 25.9 | 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
- ALPI
- Protein
- p.Pro94Ser
- Coding
- c.280C>T
- MANE Select
- NM_001631
- Type
- single nucleotide variant
- Location
- chr2:232456675 (GRCh38)
- Gene constraint
- LOEUF 1.163 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.46
Similar variants
- ALPI p.Ala97Thr Uncertain significance ★★ ⚠ same type
- ALPI p.Arg299Ter Uncertain significance ★★ same type
- ALPI p.Gln171Arg Uncertain significance ★★ ⚠ same type
- ALPI p.Glu449Asp Uncertain significance ★★ ⚠ same type
- ALPI p.Leu9Pro Uncertain significance ★★ ⚠ same type
- ALPI p.Pro28Leu Uncertain significance ★★ ⚠ same type
- ALPI p.Arg92Cys Likely benign ★★ ⚠ same type
- ALPI p.Asp248= Likely benign ★★ 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/alpi-p-pro94ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown