Is OVCA2 p.Arg5Gln (c.14G>A) pathogenic?

OVCA2 p.Arg5Gln (c.14G>A) is classified Likely benign in OVCA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-03). AlphaMissense: likely benign (0.1041); No allele count reported in gnomAD v4.1 (AN 1,540,240).

How common is OVCA2 p.Arg5Gln (c.14G>A) in the general population?

OVCA2 p.Arg5Gln (c.14G>A) is no allele count reported in gnomAD v4.1 (AN 1,540,240) (gnomAD).

What do computational predictors say about OVCA2 p.Arg5Gln (c.14G>A)?

AlphaMissense predicts likely benign (score 0.1041) — an in-silico prediction, not a clinical call.

OVCA2 p.Arg5Gln

c.14G>A · VCV4129524

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1041 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,540,240)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1041	likely benign
REVEL	0.05	moderately benign-leaning
SaProt	LLR -9.64	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -5.2	GERP -4.6
Regional constraint	o/e 1.25	unconstrained · MANE · 1,053 bp · p 1.3e-05 · regional, not allelic
Overall
CADD	0.033	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

No allele count reported in gnomAD v4.1 (AN 1,540,240). 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: OVCA2
Protein: p.Arg5Gln
Coding: c.14G>A
MANE Select: NM_001383 · reported on NM_080822
Type: single nucleotide variant
Location: chr17:2042061 (GRCh38)

Full OVCA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/ovca2-p-arg5gln (accessed [today's date]).

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