Is NOVA2 p.Tyr330fs (c.987del) pathogenic?

NOVA2 p.Tyr330fs (c.987del) is classified Pathogenic in NOVA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-06). No gnomAD frequency available for this variant; Associated with neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities.

How common is NOVA2 p.Tyr330fs (c.987del) in the general population?

NOVA2 p.Tyr330fs (c.987del) is no gnomAD frequency available for this variant (gnomAD).

NOVA2 p.Tyr330fs

Q: What condition is associated with NOVA2 p.Tyr330fs (c.987del)?

NOVA2 p.Tyr330fs (c.987del) is associated with neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities (ClinVar).

c.987del · rs2513852016 · VCV3068386

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 10	GERP 2.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: NOVA2
Protein: p.Tyr330fs
Coding: c.987del
MANE Select: NM_002516
dbSNP: rs2513852016
Type: Deletion
Location: chr19:45940355 (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

neurodevelopmental disorder with or without autistic features and/or structural brain abnormalities — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NOVA2 p.Gly219fs Likely pathogenic ★ same condition
NOVA2 p.Leu175fs Pathogenic ★ same condition
NOVA2 p.Val261fs Pathogenic ★ same condition
NOVA2 c.41_85+14del Uncertain significance ★ same condition
NOVA2 p.Ala314_Ala316del Uncertain significance ★ same condition
NOVA2 p.Val237fs Pathogenic same condition
NOVA2 p.Ala287= Benign ★★ same condition
NOVA2 p.Leu238= 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-tyr330fs (accessed [today's date]).

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