Is CCPG1 p.Pro802Ser (c.2404C>T) pathogenic?

CCPG1 p.Pro802Ser (c.2404C>T) is classified Uncertain significance in CCPG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-01). Very rare (popmax 0.00198%, amr).

How common is CCPG1 p.Pro802Ser (c.2404C>T) in the general population?

CCPG1 p.Pro802Ser (c.2404C>T) is very rare (popmax 0.00198%, amr) (gnomAD).

CCPG1 p.Pro802Ser

c.2404C>T · VCV4650181

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00198%, amr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.339	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,524 bp · p 0.009 · regional, not allelic
Overall
CADD	25.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00198% Admixed American · 1/50,438 alleles

Filtering AF 8.2e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.5e-05%

Overall 0.000326% 5/1,533,848 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00198%	50,438
European (non-Finnish)	0.000349%	286,517

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: CCPG1
Protein: p.Pro802Ser
Coding: c.2404C>T
MANE Select: NM_001204450
Type: single nucleotide variant
Location: chr15:55356240 (GRCh38)
Gene constraint: LOEUF 0.777 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.96 · 1 PDB

Full CCPG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PIGB p.Ile537Met Pathogenic/Likely pathogenic ★★ ⚠ same type
PIGB p.Lys551Thr Benign ★★ same type
PIGB p.Ser509= Benign ★★ same type
CCPG1 p.Ala576Val Uncertain significance ★ ⚠ same type
CCPG1 p.Ala75Thr Uncertain significance ★ ⚠ same type
CCPG1 p.Arg179His Uncertain significance ★ ⚠ same type
CCPG1 p.Arg193Gln Uncertain significance ★ ⚠ same type
CCPG1 p.Arg193Trp 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/ccpg1-p-pro802ser (accessed [today's date]).

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