Is MCM4 p.Phe824Ser (c.2471T>C) pathogenic?

MCM4 p.Phe824Ser (c.2471T>C) is classified Uncertain significance in MCM4 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-22). AlphaMissense: ambiguous (0.4417); Ultra-rare (popmax 0.0111%, amr).

How common is MCM4 p.Phe824Ser (c.2471T>C) in the general population?

MCM4 p.Phe824Ser (c.2471T>C) is ultra-rare (popmax 0.0111%, amr) (gnomAD).

What do computational predictors say about MCM4 p.Phe824Ser (c.2471T>C)?

AlphaMissense predicts ambiguous (score 0.4417) — an in-silico prediction, not a clinical call.

MCM4 p.Phe824Ser

c.2471T>C · VCV4550481

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4417 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0111%, amr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4417	ambiguous
REVEL	0.268	benign-leaning
SaProt	LLR -13.53	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP 2.4, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 3,808 bp · p 0.82 · regional, not allelic
Overall
CADD	29.2	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

Grpmax group 0.0111% Admixed American · 6/53,864 alleles

Filtering AF 0.00479% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00322%

Overall 0.000568% 9/1,583,668 alleles · ultra-rare exomes 8/1,431,398 · genomes 1/152,270 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0111%	8,977
European (non-Finnish)	0.000257%	389,736

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.Phe824Ser
Coding: c.2471T>C
MANE Select: NM_182746
Type: single nucleotide variant
Location: chr8:47975820 (GRCh38)
Gene constraint: LOEUF 0.806 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.25 · 28 PDB
Residue 824: an α-helix

Full MCM4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-phe824ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown