Is NOVA2 p.Arg439His (c.1316G>A) pathogenic?

NOVA2 p.Arg439His (c.1316G>A) is classified Uncertain significance in NOVA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-23). AlphaMissense: likely pathogenic (0.9127); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with NOVA2 p.Arg439His (c.1316G>A)?

NOVA2 p.Arg439His (c.1316G>A) is associated with Inborn genetic diseases (ClinVar).

How common is NOVA2 p.Arg439His (c.1316G>A) in the general population?

NOVA2 p.Arg439His (c.1316G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NOVA2 p.Arg439His (c.1316G>A)?

AlphaMissense predicts likely pathogenic (score 0.9127) — an in-silico prediction, not a clinical call.

NOVA2 p.Arg439His

c.1316G>A · VCV4861139

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9127 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9127	likely pathogenic
REVEL	0.224	benign-leaning
SaProt	LLR -9.97	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 0.76, phastCons 1
Regional constraint	o/e 0.32	constrained · MANE · 238 bp · p 4.8e-12 · regional, not allelic
Overall
CADD	32.0	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NOVA2
Protein: p.Arg439His
Coding: c.1316G>A
MANE Select: NM_002516
Type: single nucleotide variant
Location: chr19:45940026 (GRCh38)
Gene constraint: LOEUF 0.611 · pLI 0.85 (gnomAD)
Structure: AlphaFold pLDDT 65.60 · 2 PDB
Residue 439: a β-strand; the kh 3 domain

Full NOVA2 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

NOVA2 p.Ala247Thr Uncertain significance ★★ ⚠ same condition
NOVA2 p.Asn292Thr Likely benign ★★ same condition
NOVA2 p.Ala240Thr Uncertain significance ★ ⚠ same condition
NOVA2 p.Ala248Pro Uncertain significance ★ ⚠ same condition
NOVA2 p.Ala331Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
NOVA2 p.Ala334Thr Conflicting classifications of pathogenicity ★ ⚠ same condition
NOVA2 p.Ala339Pro Uncertain significance ★ ⚠ same condition
NOVA2 p.Ala362Thr 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/nova2-p-arg439his (accessed [today's date]).

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