Is ARRDC1 p.Val30Leu (c.88G>C) pathogenic?

ARRDC1 p.Val30Leu (c.88G>C) is classified Uncertain significance in ARRDC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-30). AlphaMissense: likely benign (0.1106); Absent from gnomAD v4.1.

How common is ARRDC1 p.Val30Leu (c.88G>C) in the general population?

ARRDC1 p.Val30Leu (c.88G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARRDC1 p.Val30Leu (c.88G>C)?

AlphaMissense predicts likely benign (score 0.1106) — an in-silico prediction, not a clinical call.

ARRDC1 p.Val30Leu

c.88G>C · VCV3316226

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1106 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,292,288)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1106	likely benign
REVEL	0.114	moderately benign-leaning
SaProt	LLR -4.56	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 4.5	GERP 0.96, phastCons 1
Regional constraint	o/e 1.10	unconstrained · MANE · 9,417 bp · p 0.014 · regional, not allelic
Overall
CADD	18.33	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

No allele count reported in gnomAD v4.1 (AN 1,292,288). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ARRDC1
Protein: p.Val30Leu
Coding: c.88G>C
MANE Select: NM_152285
Type: single nucleotide variant
Location: chr9:137605805 (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.Val30Met Uncertain significance ★ ⚠ same residue
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

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-val30leu (accessed [today's date]).

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