Is CPXM1 p.Pro477Ala (c.1429C>G) pathogenic?

CPXM1 p.Pro477Ala (c.1429C>G) is classified Uncertain significance in CPXM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-07). AlphaMissense: likely benign (0.1032); Very rare (popmax 0.000255%, nfe).

How common is CPXM1 p.Pro477Ala (c.1429C>G) in the general population?

CPXM1 p.Pro477Ala (c.1429C>G) is very rare (popmax 0.000255%, nfe) (gnomAD).

What do computational predictors say about CPXM1 p.Pro477Ala (c.1429C>G)?

AlphaMissense predicts likely benign (score 0.1032) — an in-silico prediction, not a clinical call.

CPXM1 p.Pro477Ala

c.1429C>G · VCV4656322

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1032 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000255%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1032	likely benign
REVEL	0.162	moderately benign-leaning
SaProt	LLR -8.62	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 12	GERP 0.73, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 6,295 bp · p 0.0064 · regional, not allelic
Overall
CADD	25.6	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

Grpmax group 0.000255% European (non-Finnish) · 3/1,176,738 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000206% 3/1,457,176 alleles · very rare

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: CPXM1
Protein: p.Pro477Ala
Coding: c.1429C>G
MANE Select: NM_019609
Type: single nucleotide variant
Location: chr20:2795890 (GRCh38)
Gene constraint: LOEUF 1.081 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.78
Residue 477: the peptidase m14 domain

Full CPXM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPXM1 p.Arg725His Uncertain significance ★★ ⚠ same type
CPXM1 p.Leu711= Benign ★★ same type
CPXM1 p.Ala108Thr Uncertain significance ★ ⚠ same type
CPXM1 p.Ala132Thr Uncertain significance ★ ⚠ same type
CPXM1 p.Ala21Pro Uncertain significance ★ ⚠ same type
CPXM1 p.Ala227Thr Uncertain significance ★ ⚠ same type
CPXM1 p.Ala269Pro Uncertain significance ★ ⚠ same type
CPXM1 p.Ala273Thr 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/cpxm1-p-pro477ala (accessed [today's date]).

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