Is ARHGAP23 p.Arg265Trp (c.793C>T) pathogenic?

ARHGAP23 p.Arg265Trp (c.793C>T) is classified Uncertain significance in ARHGAP23 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-24). AlphaMissense: likely benign (0.1418); Ultra-rare (popmax 0.0246%, eas).

How common is ARHGAP23 p.Arg265Trp (c.793C>T) in the general population?

ARHGAP23 p.Arg265Trp (c.793C>T) is ultra-rare (popmax 0.0246%, eas) (gnomAD).

What do computational predictors say about ARHGAP23 p.Arg265Trp (c.793C>T)?

AlphaMissense predicts likely benign (score 0.1418) — an in-silico prediction, not a clinical call.

ARHGAP23 p.Arg265Trp

c.793C>T · rs754961345 · VCV2516575

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1418 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0246%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1418	likely benign
REVEL	0.092	moderately benign-leaning
SaProt	LLR -8.04	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 1.6, phastCons 1
Overall
CADD	22.2	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 0.0246% East Asian · 10/40,682 alleles

Filtering AF 0.0133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0101%

Overall 0.00303% 46/1,518,296 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0246%	4,068
South Asian	0.0148%	6,771
Remaining individualsnot grpmax-eligible	0.00507%	19,705
Admixed American	0.00202%	49,576
European (non-Finnish)	0.00167%	59,783
African / African-American	0.00137%	72,806

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: ARHGAP23
Protein: p.Arg265Trp
Coding: c.793C>T
MANE Select: NM_001199417
dbSNP: rs754961345
Type: single nucleotide variant
Location: chr17:38466476 (GRCh38)
Gene constraint: LOEUF 0.414 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 49.82
Residue 265: the 'disordered' region

Full ARHGAP23 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

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ARHGAP23 p.Ala1222Val Uncertain significance ★ ⚠ same type
ARHGAP23 p.Ala1324Val Uncertain significance ★ ⚠ same type
ARHGAP23 p.Ala1340Thr Uncertain significance ★ ⚠ same type
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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/arhgap23-p-arg265trp (accessed [today's date]).

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