Is CPD p.Pro229Ala (c.685C>G) pathogenic?

CPD p.Pro229Ala (c.685C>G) is classified Uncertain significance in CPD (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-04). AlphaMissense: likely benign (0.0617); Rare (popmax 0.103%, amr).

How common is CPD p.Pro229Ala (c.685C>G) in the general population?

CPD p.Pro229Ala (c.685C>G) is rare (popmax 0.103%, amr) (gnomAD).

What do computational predictors say about CPD p.Pro229Ala (c.685C>G)?

AlphaMissense predicts likely benign (score 0.0617) — an in-silico prediction, not a clinical call.

CPD p.Pro229Ala

c.685C>G · rs530282755 · VCV2545030

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0617 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.103%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0617	likely benign
REVEL	0.117	moderately benign-leaning
SaProt	LLR -6.77	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	GERP 0.17, phastCons 1
Overall
CADD	18.15	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 0.103% Admixed American · 44/42,874 alleles

Filtering AF 0.0818% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.08%

Overall 0.0717% 1,091/1,521,694 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.103%	974
European (non-Finnish)	0.0862%	1,159
Finnishnot grpmax-eligible	0.0488%	2,051
Remaining individualsnot grpmax-eligible	0.0426%	2,345
African / African-American	0.00878%	11,388

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: CPD
Protein: p.Pro229Ala
Coding: c.685C>G
MANE Select: NM_004839 · reported on NM_001304
dbSNP: rs530282755
Type: single nucleotide variant
Location: chr17:30379665 (GRCh38)
Structure: AlphaFold pLDDT 89.20

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

Similar variants

CPD p.Pro229Ser Uncertain significance ★ ⚠ same residue
CPD p.Pro229Thr Uncertain significance ★ ⚠ same residue
HOMER2 p.Arg208Cys Uncertain significance ★★ ⚠ same type
HOMER2 p.Arg213Trp Uncertain significance ★★ ⚠ same type
HOMER2 p.Arg215His Uncertain significance ★★ ⚠ same type
HOMER2 p.Arg309Cys Uncertain significance ★★ ⚠ same type
HOMER2 p.Arg334Gln Uncertain significance ★★ ⚠ same type
HOMER2 p.Asn235Lys 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/cpd-p-pro229ala (accessed [today's date]).

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