Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ALKALINE PHOSPHATASE, PLACENTAL, ALLELE-1 POLYMORPHISM
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 3.9 | GERP 1.9, phastCons 1 |
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
- ALPP
- Protein
- p.Pro25=
- Coding
- c.74C=
- MANE Select
- NM_001632
- dbSNP
- rs1130335
- Type
- single nucleotide variant
- Location
- chr2:232378876 (GRCh38)
- Gene constraint
- LOEUF 1.117 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.73 · 8 PDB
- Residue 25
- a UniProt-annotated variant site (in)
Disease context
ALKALINE PHOSPHATASE, PLACENTAL, ALLELE-1 POLYMORPHISM
Similar variants
- ALPP p.Pro25Leu Benign ★ ⚠ same residue
- ALPP c.865+8C>T Likely benign ★★ same type
- ALPP p.Ala176= Benign ★★ same type
- ALPP p.Arg231Pro Benign ★★ same type
- ALPP p.Arg36= Benign ★★ same type
- ALPP p.Glu37Gln Benign ★★ same type
- ALPP p.Gly233= Likely benign ★★ same type
- ALPP p.Gly63= 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/alpp-p-pro25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown