Is PCGF2 p.Pro339= (c.1017C>T) pathogenic?

PCGF2 p.Pro339= (c.1017C>T) is classified Likely benign in PCGF2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-11-22). Rare (popmax 0.332%, mid).

How common is PCGF2 p.Pro339= (c.1017C>T) in the general population?

PCGF2 p.Pro339= (c.1017C>T) is rare (popmax 0.332%, mid) (gnomAD).

PCGF2 p.Pro339=

c.1017C>T · rs112908318 · VCV1633188

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.332%, mid)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -0.8	GERP -4.5
Overall
CADD	0.834	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.332% Middle Eastern · 18/5,428 alleles

Filtering AF 0.214% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.177%

Overall 0.0101% 146/1,442,892 alleles · rare exomes 130/1,290,606 · genomes 16/152,286 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.332%	302
African / African-American	0.0779%	1,284
Remaining individualsnot grpmax-eligible	0.0454%	2,202
Admixed American	0.00513%	19,500
European (non-Finnish)	0.00405%	24,708
East Asian	0.00254%	39,340
South Asian	0.00147%	68,188

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: PCGF2
Protein: p.Pro339=
Coding: c.1017C>T
MANE Select: NM_007144
dbSNP: rs112908318
Type: single nucleotide variant
Location: chr17:38735241 (GRCh38)

Full PCGF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/pcgf2-p-pro339 (accessed [today's date]).

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