Is CCPG1 p.Phe700Leu (c.2100T>G) pathogenic?

CCPG1 p.Phe700Leu (c.2100T>G) is classified Uncertain significance in CCPG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-15). AlphaMissense: likely pathogenic (0.9902); Absent from gnomAD v4.1.

How common is CCPG1 p.Phe700Leu (c.2100T>G) in the general population?

CCPG1 p.Phe700Leu (c.2100T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CCPG1 p.Phe700Leu (c.2100T>G)?

AlphaMissense predicts likely pathogenic (score 0.9902) — an in-silico prediction, not a clinical call.

CCPG1 p.Phe700Leu

c.2100T>G · VCV3829195

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9902 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.9902	likely pathogenic · top 1% in CCPG1
REVEL	0.441	indeterminate
SaProt	LLR -7.66	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.1	GERP 2.6, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 3,524 bp · p 0.009 · regional, not allelic
Overall
CADD	22.4	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: CCPG1
Protein: p.Phe700Leu
Coding: c.2100T>G
MANE Select: NM_001204450
Type: single nucleotide variant
Location: chr15:55359673 (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-phe700leu (accessed [today's date]).

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