Is NOVA2 p.Ala384= (c.1152T>G) pathogenic?

NOVA2 p.Ala384= (c.1152T>G) is classified Likely benign in NOVA2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-04-26). Absent from gnomAD v4.1; Associated with NOVA2-related disorder.

What condition is associated with NOVA2 p.Ala384= (c.1152T>G)?

NOVA2 p.Ala384= (c.1152T>G) is associated with NOVA2-related disorder (ClinVar).

How common is NOVA2 p.Ala384= (c.1152T>G) in the general population?

NOVA2 p.Ala384= (c.1152T>G) is absent from gnomAD v4.1 (gnomAD).

NOVA2 p.Ala384=

c.1152T>G · rs2513851778 · VCV3038009

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

NOVA2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.1	GERP -3.2
Overall
CADD	0.517	PHRED · no single calibrated threshold — expert panels disagree

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.Ala384=
Coding: c.1152T>G
MANE Select: NM_002516
dbSNP: rs2513851778
Type: single nucleotide variant
Location: chr19:45940190 (GRCh38)
Gene constraint: LOEUF 0.611 · pLI 0.85 (gnomAD)
Structure: AlphaFold pLDDT 65.60 · 2 PDB

Full NOVA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NOVA2-related disorder

Similar variants

NOVA2 p.Val237Ala Uncertain significance ★ ⚠ same condition
NOVA2 p.Ala385= Likely benign same condition
NOVA2 p.Ala386= Likely benign same condition
NOVA2 p.Gly377= Likely benign same condition
NOVA2 p.Gly369fs Likely pathogenic ★ same condition
NOVA2 p.Leu276fs Likely pathogenic ★ same condition
NOVA2 p.Ser404fs Uncertain significance same condition
NOVA2 p.Ala324del Likely benign 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-ala384 (accessed [today's date]).

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