Is ARHGAP31 p.Asp845Val (c.2534A>T) pathogenic?

ARHGAP31 p.Asp845Val (c.2534A>T) is classified Likely benign in ARHGAP31 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-01-30). AlphaMissense: likely benign (0.1117); Rare (popmax 0.12%, afr); Associated with Inborn genetic diseases.

What condition is associated with ARHGAP31 p.Asp845Val (c.2534A>T)?

ARHGAP31 p.Asp845Val (c.2534A>T) is associated with Inborn genetic diseases (ClinVar).

How common is ARHGAP31 p.Asp845Val (c.2534A>T) in the general population?

ARHGAP31 p.Asp845Val (c.2534A>T) is rare (popmax 0.12%, afr) (gnomAD).

What do computational predictors say about ARHGAP31 p.Asp845Val (c.2534A>T)?

AlphaMissense predicts likely benign (score 0.1117) — an in-silico prediction, not a clinical call.

ARHGAP31 p.Asp845Val

c.2534A>T · rs199843927 · VCV1532715

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1117 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.12%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1117	likely benign
REVEL	0.071	moderately benign-leaning
SaProt	LLR -6.08	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 5.9	GERP 1.5, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 121 kb · p 1.9e-07 · regional, not allelic
Overall
CADD	20.3	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.12% African / African-American · 90/74,942 alleles

Filtering AF 0.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0926%

Overall 0.0062% 100/1,614,122 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.12%	833
Remaining individualsnot grpmax-eligible	0.0112%	8,927
Admixed American	0.00333%	30,004
European (non-Finnish)	8.47e-05%	1,180,043

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: ARHGAP31
Protein: p.Asp845Val
Coding: c.2534A>T
MANE Select: NM_020754
dbSNP: rs199843927
Type: single nucleotide variant
Location: chr3:119414463 (GRCh38)
Gene constraint: LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 43.32
Residue 845: the 'disordered' region

Full ARHGAP31 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARHGAP31 p.Ala18Val Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Ala634Asp Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg1377Ser Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg199Gln Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg256Cys Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg478His Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg510Ser Uncertain significance ★★ ⚠ same condition
ARHGAP31 p.Arg950Cys Uncertain significance ★★ ⚠ 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/arhgap31-p-asp845val (accessed [today's date]).

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