Is PCGF2 p.Arg331His (c.992G>A) pathogenic?

PCGF2 p.Arg331His (c.992G>A) is classified Uncertain significance in PCGF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-25). AlphaMissense: likely benign (0.3132); Ultra-rare (popmax 0.021%, afr); Associated with Inborn genetic diseases.

What condition is associated with PCGF2 p.Arg331His (c.992G>A)?

PCGF2 p.Arg331His (c.992G>A) is associated with Inborn genetic diseases (ClinVar).

How common is PCGF2 p.Arg331His (c.992G>A) in the general population?

PCGF2 p.Arg331His (c.992G>A) is ultra-rare (popmax 0.021%, afr) (gnomAD).

What do computational predictors say about PCGF2 p.Arg331His (c.992G>A)?

AlphaMissense predicts likely benign (score 0.3132) — an in-silico prediction, not a clinical call.

PCGF2 p.Arg331His

c.992G>A · VCV4627069

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3132 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.021%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.3132	likely benign
REVEL	0.115	moderately benign-leaning
SaProt	LLR -7.58	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 5.9	GERP 1.2, phastCons 1
Overall
CADD	23.1	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 0.021% African / African-American · 15/71,326 alleles

Filtering AF 0.0129% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0105%

Overall 0.00136% 20/1,465,990 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.021%	4,755
Remaining individualsnot grpmax-eligible	0.00178%	56,106
European (non-Finnish)	0.000364%	274,578

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.Arg331His
Coding: c.992G>A
MANE Select: NM_001136498 · reported on NM_007144
Type: single nucleotide variant
Location: chr17:38735266 (GRCh38)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-arg331his (accessed [today's date]).

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