Is PCGF2 p.Ser260= (c.780C>T) pathogenic?

PCGF2 p.Ser260= (c.780C>T) is classified Likely benign in PCGF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-19). Ultra-rare (popmax 0.0283%, afr).

How common is PCGF2 p.Ser260= (c.780C>T) in the general population?

PCGF2 p.Ser260= (c.780C>T) is ultra-rare (popmax 0.0283%, afr) (gnomAD).

PCGF2 p.Ser260=

c.780C>T · VCV3717807

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0283%, afr)

⚠ 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 3.3	GERP -0.041, phastCons 1
Overall
CADD	10.32	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0283% African / African-American · 21/74,314 alleles

Filtering AF 0.0189% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0158%

Overall 0.00201% 32/1,591,900 alleles · ultra-rare exomes 22/1,440,306 · genomes 10/151,594 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0283%	3,539
South Asian	0.00455%	21,954
Remaining individualsnot grpmax-eligible	0.00325%	30,796
Admixed American	0.00176%	56,830
European (non-Finnish)	0.000342%	292,405

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.Ser260=
Coding: c.780C>T
MANE Select: NM_007144
Type: single nucleotide variant
Location: chr17:38735478 (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-ser260 (accessed [today's date]).

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