MCM3AP p.Ser656=
c.1968C>T · rs534696205 · VCV1665415
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.412%, sas)
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 -1.4 | GERP -3.6 |
| Overall | ||
| CADD | 0.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.412%
South Asian · 375/91,034 alleles
Filtering AF
0.377%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.364%
Overall
0.0257%
415/1,613,834 alleles · rare
exomes 391/1,461,606 · genomes 24/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.412% | 243 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Admixed American | 0.00333% | 29,992 |
| African / African-American | 0.00133% | 75,014 |
| European (non-Finnish) | 0.000932% | 107,263 |
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.Ser656=
- Coding
- c.1968C>T
- MANE Select
- NM_003906
- dbSNP
- rs534696205
- Type
- single nucleotide variant
- Location
- chr21:46275216 (GRCh38)
- Gene constraint
- LOEUF 0.769 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.83 · 7 PDB
Similar variants
- MCM3AP p.Ser656Arg 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-ser656 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown