Is ARAP3 p.Arg936Trp (c.2806C>T) pathogenic?

ARAP3 p.Arg936Trp (c.2806C>T) is classified Uncertain significance in ARAP3 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: ambiguous (0.4195); Very rare (popmax 0.00167%, amr); Associated with prostate cancer.

What condition is associated with ARAP3 p.Arg936Trp (c.2806C>T)?

ARAP3 p.Arg936Trp (c.2806C>T) is associated with prostate cancer (ClinVar).

How common is ARAP3 p.Arg936Trp (c.2806C>T) in the general population?

ARAP3 p.Arg936Trp (c.2806C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

What do computational predictors say about ARAP3 p.Arg936Trp (c.2806C>T)?

AlphaMissense predicts ambiguous (score 0.4195) — an in-silico prediction, not a clinical call.

ARAP3 p.Arg936Trp

c.2806C>T · rs145752053 · VCV161761

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4195 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

prostate cancer

Computational evidence

Protein change
AlphaMissense	0.4195	ambiguous
REVEL	0.208	benign-leaning
SaProt	LLR -8.60	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 0.3, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 18 kb · p 1.3e-06 · regional, not allelic
Overall
CADD	27.3	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 0.00167% Admixed American · 1/59,984 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.00062% 10/1,613,766 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,984
South Asian	0.0011%	91,080
European (non-Finnish)	0.000678%	147,497

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: ARAP3
Protein: p.Arg936Trp
Coding: c.2806C>T
MANE Select: NM_022481
dbSNP: rs145752053
Type: single nucleotide variant
Location: chr5:141662250 (GRCh38)
Gene constraint: LOEUF 0.598 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.20 · 7 PDB
Residue 936: the rho-gap domain; a turn

Full ARAP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

prostate cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ARAP3 p.Ala1045Val Uncertain significance ★ ⚠ same type
ARAP3 p.Ala10Thr Uncertain significance ★ ⚠ same type
ARAP3 p.Ala1159Val Uncertain significance ★ ⚠ same type
ARAP3 p.Ala1276Ser Uncertain significance ★ ⚠ same type
ARAP3 p.Ala1342Thr Uncertain significance ★ ⚠ same type
ARAP3 p.Ala216Asp Uncertain significance ★ ⚠ same type
ARAP3 p.Ala22Val Uncertain significance ★ ⚠ same type
ARAP3 p.Ala36Thr Uncertain significance ★ ⚠ same type

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/arap3-p-arg936trp (accessed [today's date]).

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