Is CAPG p.Pro111fs (c.332del) pathogenic?

CAPG p.Pro111fs (c.332del) is classified Benign in CAPG (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Rare (popmax 0.988%, afr).

How common is CAPG p.Pro111fs (c.332del) in the general population?

CAPG p.Pro111fs (c.332del) is rare (popmax 0.988%, afr) (gnomAD).

CAPG p.Pro111fs

c.332del · rs372064925 · VCV785969

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

rare (popmax 0.988%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -9.7	GERP -4.7
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.988% African / African-American · 741/75,010 alleles

Filtering AF 0.929% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.905%

Overall 0.0483% 780/1,614,054 alleles · rare exomes 355/1,461,860 · genomes 425/152,194 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.988%	101
Remaining individualsnot grpmax-eligible	0.0368%	2,718
Admixed American	0.0233%	4,287
South Asian	0.0011%	91,082
European (non-Finnish)	8.47e-05%	1,179,967

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: CAPG
Protein: p.Pro111fs
Coding: c.332del
MANE Select: NM_001747
dbSNP: rs372064925
Type: Deletion
Location: chr2:85401548 (GRCh38)
Gene constraint: LOEUF 0.947 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.89 · 2 PDB

Full CAPG 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/capg-p-pro111fs (accessed [today's date]).

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