Is ARRDC1 p.Ala270Val (c.809C>T) pathogenic?

ARRDC1 p.Ala270Val (c.809C>T) is classified Likely benign in ARRDC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-02). AlphaMissense: likely benign (0.0643); Very rare (popmax 0.005%, amr).

How common is ARRDC1 p.Ala270Val (c.809C>T) in the general population?

ARRDC1 p.Ala270Val (c.809C>T) is very rare (popmax 0.005%, amr) (gnomAD).

What do computational predictors say about ARRDC1 p.Ala270Val (c.809C>T)?

AlphaMissense predicts likely benign (score 0.0643) — an in-silico prediction, not a clinical call.

ARRDC1 p.Ala270Val

c.809C>T · rs923558304 · VCV2514164

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0643 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.005%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0643	likely benign
REVEL	0.051	moderately benign-leaning
SaProt	LLR -6.03	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.25	acceptor gain · deltas
Constraint at this position
Conservation	phyloP -0.11	GERP -3.1
Regional constraint	o/e 1.10	unconstrained · MANE · 9,417 bp · p 0.014 · regional, not allelic
Overall
CADD	16.0	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 0.005% Admixed American · 3/59,990 alleles

Filtering AF 0.00133% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000668%

Overall 0.00105% 17/1,612,952 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.005%	19,997
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,598
Remaining individualsnot grpmax-eligible	0.0032%	31,232
East Asian	0.00223%	44,862
African / African-American	0.00133%	74,928
South Asian	0.0011%	91,092
European (non-Finnish)	0.000678%	147,493

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: ARRDC1
Protein: p.Ala270Val
Coding: c.809C>T
MANE Select: NM_152285
dbSNP: rs923558304
Type: single nucleotide variant
Location: chr9:137614572 (GRCh38)
Gene constraint: LOEUF 1.191 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.34

Full ARRDC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARRDC1 p.Ala223Val Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala228Val Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala25Ser Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala285Thr Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala311Thr Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala34Val Uncertain significance ★ ⚠ same type
ARRDC1 p.Ala94Val Uncertain significance ★ ⚠ same type
ARRDC1 p.Arg119Gln 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/arrdc1-p-ala270val (accessed [today's date]).

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