Is ARHGAP32 p.Ser366= (c.1098T>C) pathogenic?

ARHGAP32 p.Ser366= (c.1098T>C) is classified Likely benign in ARHGAP32 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Rare (popmax 0.256%, sas); Associated with ARHGAP32-related disorder.

What condition is associated with ARHGAP32 p.Ser366= (c.1098T>C)?

ARHGAP32 p.Ser366= (c.1098T>C) is associated with ARHGAP32-related disorder (ClinVar).

How common is ARHGAP32 p.Ser366= (c.1098T>C) in the general population?

ARHGAP32 p.Ser366= (c.1098T>C) is rare (popmax 0.256%, sas) (gnomAD).

ARHGAP32 p.Ser366=

c.1098T>C · rs535110024 · VCV3046261

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.256%, sas)

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 5.2	GERP -1.2, phastCons 1
Overall
CADD	12.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.256% South Asian · 220/86,040 alleles

Filtering AF 0.228% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.217%

Overall 0.014% 224/1,595,138 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.256%	391
Middle Eastern	0.0166%	6,014
Remaining individualsnot grpmax-eligible	0.00487%	20,543

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.Ser366=
Coding: c.1098T>C
MANE Select: NM_001378024
dbSNP: rs535110024
Type: single nucleotide variant
Location: chr11:128998416 (GRCh38)
Gene constraint: LOEUF 0.349 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 43.67 · 2 PDB

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-ser366 (accessed [today's date]).

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