Is ARHGAP32 p.Pro1694= (c.5082C>T) pathogenic?

ARHGAP32 p.Pro1694= (c.5082C>T) is classified Likely benign in ARHGAP32 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-12-02). Ultra-rare (popmax 0.065%, amr); Associated with ARHGAP32-related disorder.

What condition is associated with ARHGAP32 p.Pro1694= (c.5082C>T)?

ARHGAP32 p.Pro1694= (c.5082C>T) is associated with ARHGAP32-related disorder (ClinVar).

How common is ARHGAP32 p.Pro1694= (c.5082C>T) in the general population?

ARHGAP32 p.Pro1694= (c.5082C>T) is ultra-rare (popmax 0.065%, amr) (gnomAD).

ARHGAP32 p.Pro1694=

c.5082C>T · rs183293077 · VCV3049136

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.065%, amr)

Conditions

ARHGAP32-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.4	GERP -4.9
Overall
CADD	2.345	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.065% Admixed American · 39/60,032 alleles

Filtering AF 0.0488% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0432%

Overall 0.0369% 595/1,614,212 alleles · ultra-rare exomes 546/1,461,888 · genomes 49/152,324 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.065%	1,539
European (non-Finnish)	0.0448%	2,231
Ashkenazi Jewishnot grpmax-eligible	0.0236%	4,229
Remaining individualsnot grpmax-eligible	0.0224%	4,465
African / African-American	0.00666%	15,010
Finnishnot grpmax-eligible	0.00156%	64,042

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: ARHGAP32
Protein: p.Pro1694=
Coding: c.5082C>T
MANE Select: NM_001378024
dbSNP: rs183293077
Type: single nucleotide variant
Location: chr11:128970131 (GRCh38)
Gene constraint: LOEUF 0.349 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 43.67 · 2 PDB
Residue 1694: the 'interaction with gab2' region; the 'interaction with fyn' region

Full ARHGAP32 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ARHGAP32-related disorder

Similar variants

ARHGAP32 p.Ala2083Val Uncertain significance ★ same condition
ARHGAP32 p.Val1495Asp Uncertain significance ★ ⚠ same condition
ARHGAP32 p.Arg39Thr Uncertain significance ⚠ same condition
ARHGAP32 p.Pro1429Arg Uncertain significance ⚠ same condition
ARHGAP32 c.1299-7A>G Likely benign same condition
ARHGAP32 c.445-5T>C Likely benign same condition
ARHGAP32 p.Ala1090= Likely benign same condition
ARHGAP32 p.Ala74Thr Benign same condition

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/arhgap32-p-pro1694 (accessed [today's date]).

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