MCM4 p.Val860=
c.2580G>T · rs558937819 · VCV2776894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00533%, afr)
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 -0.85 | GERP -4.8, phastCons 0.003 |
| Overall | ||
| CADD | 0.614 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00533%
African / African-American · 4/75,026 alleles
Filtering AF
0.00174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.000248%
4/1,612,208 alleles · very rare
exomes 2/1,459,878 · genomes 2/152,330 · 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
- MCM4
- Protein
- p.Val860=
- Coding
- c.2580G>T
- MANE Select
- NM_182746
- dbSNP
- rs558937819
- Type
- single nucleotide variant
- Location
- chr8:47976766 (GRCh38)
- Gene constraint
- LOEUF 0.806 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.25 · 28 PDB
- Residue 860
- a β-strand
Similar variants
- MCM4 c.71-2A>G Pathogenic ★★ same type
- MCM4 c.-74C>T Uncertain significance ★★ same type
- MCM4 c.*56G>A Uncertain significance ★★ same type
- MCM4 p.Ala141Gly Uncertain significance ★★ ⚠ same type
- MCM4 p.Ala436Thr Uncertain significance ★★ ⚠ same type
- MCM4 p.Ala668Thr Uncertain significance ★★ ⚠ same type
- MCM4 p.Ala685Val Uncertain significance ★★ ⚠ same type
- MCM4 p.Ala694Thr 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/mcm4-p-val860 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown