ALPL p.Ala487=
c.1461A>C · rs2148195162 · VCV1554912
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -7.2 | GERP -3.6 |
| Overall | ||
| CADD | 0.036 | PHRED · no single calibrated threshold — expert panels disagree |
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
- ALPL
- Protein
- p.Ala487=
- Coding
- c.1461A>C
- MANE Select
- NM_000478
- dbSNP
- rs2148195162
- Type
- single nucleotide variant
- Location
- chr1:21577534 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.74 · 5 PDB
- Residue 487
- an α-helix
Similar variants
- ALPL p.Ala487Val Pathogenic/Likely pathogenic ★★ ⚠ same residue
- ALPL c.1190-2A>T Pathogenic ★★ same type
- ALPL c.182-1G>A Pathogenic/Likely pathogenic ★★ same type
- ALPL c.182-2A>G Pathogenic/Likely pathogenic ★★ same type
- ALPL c.297+1G>A Pathogenic/Likely pathogenic ★★ same type
- ALPL c.298-1G>A Pathogenic ★★ same type
- ALPL c.472+1G>A Pathogenic ★★ same type
- ALPL c.62-1G>C 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/alpl-p-ala487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown