Is CENPM p.Pro11Arg (c.32C>G) pathogenic?

CENPM p.Pro11Arg (c.32C>G) is classified Uncertain significance in CENPM (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-04). AlphaMissense: ambiguous (0.524); Absent from gnomAD v4.1.

How common is CENPM p.Pro11Arg (c.32C>G) in the general population?

CENPM p.Pro11Arg (c.32C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CENPM p.Pro11Arg (c.32C>G)?

AlphaMissense predicts ambiguous (score 0.524) — an in-silico prediction, not a clinical call.

CENPM p.Pro11Arg

c.32C>G · VCV3490394

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.524 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.524	ambiguous
REVEL	0.443	indeterminate
SaProt	LLR -5.86	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 8,017 bp · p 0.48 · regional, not allelic
Overall
CADD	25.8	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

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: CENPM
Protein: p.Pro11Arg
Coding: c.32C>G
MANE Select: NM_024053
Type: single nucleotide variant
Location: chr22:41947045 (GRCh38)
Gene constraint: LOEUF 1.038 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.38 · 14 PDB

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

Similar variants

CENPM p.Ala16Asp Uncertain significance ★ ⚠ same type
CENPM p.Arg106Trp Uncertain significance ★ ⚠ same type
CENPM p.Arg114Trp Uncertain significance ★ ⚠ same type
CENPM p.Arg145His Uncertain significance ★ ⚠ same type
CENPM p.Arg148His Uncertain significance ★ ⚠ same type
CENPM p.Arg86Pro Uncertain significance ★ ⚠ same type
CENPM p.Asn14Ser Uncertain significance ★ ⚠ same type
CENPM p.Cys131Ser 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/cenpm-p-pro11arg (accessed [today's date]).

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