ALCAM p.Pro42Ser
c.124C>T · VCV4639881
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.4297 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.4297 | ambiguous |
|---|---|---|
| REVEL | 0.384 | indeterminate |
| SaProt | LLR -10.35 | damaging |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.7, phastCons 1 |
| Regional constraint | o/e 0.95 | unconstrained · MANE · 180 kb · p 0.27 · regional, not allelic |
| Overall | ||
| CADD | 26.4 | 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
- ALCAM
- Protein
- p.Pro42Ser
- Coding
- c.124C>T
- MANE Select
- NM_001627
- Type
- single nucleotide variant
- Location
- chr3:105520117 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13 · 1 PDB
- Residue 42
- the ig-like v-type 1 domain
Similar variants
- ALCAM p.Pro42Leu Uncertain significance ★ ⚠ same residue
- ALCAM p.Asp81= Benign ★★ same type
- ALCAM p.His508= Benign/Likely benign ★★ same type
- ALCAM p.Leu254= Benign ★★ same type
- ALCAM p.Pro84Leu Benign ★★ ⚠ same type
- ALCAM p.Ser454= Benign/Likely benign ★★ same type
- ALCAM p.Thr301Met Benign ★★ ⚠ same type
- ALCAM p.Tyr224= 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/alcam-p-pro42ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown