MCM3AP p.Ala487=
c.1461T>C · rs2517426794 · VCV1916815
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.9 | GERP -2.1 |
| Overall | ||
| CADD | 5.001 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,030 alleles
Overall
6.2e-05%
1/1,612,738 alleles · very rare
exomes 1/1,460,368 · genomes 0/152,370 · joint denominator
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
- MCM3AP
- Protein
- p.Ala487=
- Coding
- c.1461T>C
- MANE Select
- NM_003906
- dbSNP
- rs2517426794
- Type
- single nucleotide variant
- Location
- chr21:46280558 (GRCh38)
- Gene constraint
- LOEUF 0.769 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.83 · 7 PDB
Similar variants
- MCM3AP p.Ala487Val Uncertain significance ★ ⚠ same residue
- MCM3AP c.3933-1G>T Likely pathogenic ★★ same type
- MCM3AP c.1443+4A>G Uncertain significance ★★ same type
- MCM3AP p.Ala1102Ser Uncertain significance ★★ ⚠ same type
- MCM3AP p.Ala1104Val Uncertain significance ★★ ⚠ same type
- MCM3AP p.Ala1117Val Uncertain significance ★★ ⚠ same type
- MCM3AP p.Ala1283Thr Uncertain significance ★★ ⚠ same type
- MCM3AP p.Ala1495Val Uncertain significance ★★ ⚠ 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/mcm3ap-p-ala487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown