MCM8 p.Ser87=
c.261C>T · rs752298258 · VCV741420
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00402%, 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 -2.1 | GERP -4.2 |
| Overall | ||
| CADD | 4.089 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00402%
African / African-American · 3/74,616 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000496%
Overall
0.000811%
13/1,602,018 alleles · very rare
exomes 12/1,449,840 · genomes 1/152,178 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00402% | 24,872 |
| East Asian | 0.00223% | 44,818 |
| European (non-Finnish) | 0.000769% | 129,977 |
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
- MCM8
- Protein
- p.Ser87=
- Coding
- c.261C>T
- MANE Select
- NM_032485
- dbSNP
- rs752298258
- Type
- single nucleotide variant
- Location
- chr20:5954615 (GRCh38)
- Gene constraint
- LOEUF 0.97 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.55 · 7 PDB
Similar variants
- MCM8 c.-5-7C>T Benign ★★ same type
- MCM8 p.Ala98Pro Benign ★★ ⚠ same type
- MCM8 p.Asn183Ser Benign ★★ same type
- MCM8 p.Asn364= Benign ★★ same type
- MCM8 p.Asp736= Benign/Likely benign ★★ same type
- MCM8 p.Cys155Tyr Benign ★★ ⚠ same type
- MCM8 p.Ile138Met Benign/Likely benign ★★ same type
- MCM8 p.Ile141Val 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/mcm8-p-ser87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown