Is MCM2 p.Ser13Arg (c.39C>G) pathogenic?

MCM2 p.Ser13Arg (c.39C>G) is classified Uncertain significance in MCM2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-15). AlphaMissense: likely benign (0.2907); Absent from gnomAD v4.1.

How common is MCM2 p.Ser13Arg (c.39C>G) in the general population?

MCM2 p.Ser13Arg (c.39C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about MCM2 p.Ser13Arg (c.39C>G)?

AlphaMissense predicts likely benign (score 0.2907) — an in-silico prediction, not a clinical call.

MCM2 p.Ser13Arg

c.39C>G · rs1201891506 · VCV1944761

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2907 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2907	likely benign
REVEL	0.129	moderately benign-leaning
SaProt	LLR -9.83	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP -1.4, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 6,632 bp · p 0.67 · regional, not allelic
Overall
CADD	20.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MCM2
Protein: p.Ser13Arg
Coding: c.39C>G
MANE Select: NM_004526
dbSNP: rs1201891506
Type: single nucleotide variant
Location: chr3:127599350 (GRCh38)
Gene constraint: LOEUF 0.706 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.54 · 39 PDB
Residue 13: a modified residue (phosphoserine); the 'disordered' region; the 'interaction with kat7' region

Full MCM2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MCM2 p.Ala148Thr Uncertain significance ★★ ⚠ same type
MCM2 p.Ala2Glu Uncertain significance ★★ ⚠ same type
MCM2 p.Ala400Thr Uncertain significance ★★ ⚠ same type
MCM2 p.Arg126Gln Uncertain significance ★★ ⚠ same type
MCM2 p.Arg149His Uncertain significance ★★ ⚠ same type
MCM2 p.Arg152His Uncertain significance ★★ ⚠ same type
MCM2 p.Arg227His Uncertain significance ★★ ⚠ same type
MCM2 p.Arg284Cys 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/mcm2-p-ser13arg (accessed [today's date]).

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