Is ARHGAP32 p.Ser896= (c.2688C>T) pathogenic?

ARHGAP32 p.Ser896= (c.2688C>T) is classified Benign in ARHGAP32 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-14). Common (popmax 5.42%, afr) — too common for a highly-penetrant pathogenic allele; Associated with ARHGAP32-related disorder.

What condition is associated with ARHGAP32 p.Ser896= (c.2688C>T)?

ARHGAP32 p.Ser896= (c.2688C>T) is associated with ARHGAP32-related disorder (ClinVar).

ARHGAP32 p.Ser896=

Q: How common is ARHGAP32 p.Ser896= (c.2688C>T) in the general population?

ARHGAP32 p.Ser896= (c.2688C>T) is common (popmax 5.42%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2688C>T · rs35287114 · VCV3056166

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 5.42%, afr) — too common for a highly-penetrant pathogenic allele

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 -1.8	GERP -5.2
Overall
CADD	0.824	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5.42% African / African-American · 4,064/75,028 alleles

Filtering AF 5.28% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.22%

Overall 1.41% 22,686/1,614,162 alleles · common exomes 19,176/1,461,886 · genomes 3,510/152,276 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5.42%	18
Amishnot grpmax-eligible	4.51%	22
Ashkenazi Jewishnot grpmax-eligible	3.47%	29
South Asian	3.46%	29
Middle Eastern	3.43%	29
Remaining individualsnot grpmax-eligible	1.71%	59
European (non-Finnish)	1.06%	94
Admixed American	0.773%	129
Finnishnot grpmax-eligible	0.201%	496
East Asian	0.0134%	7,482

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.Ser896=
Coding: c.2688C>T
MANE Select: NM_001378024
dbSNP: rs35287114
Type: single nucleotide variant
Location: chr11:128974509 (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-ser896 (accessed [today's date]).

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