NOVA2 p.Ala324del
c.958GCC[4] · rs771592016 · VCV3060845
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.083%, sas)
Conditions
1
NOVA2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.2 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 17.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.083%
South Asian · 59/71,088 alleles
Filtering AF
0.066%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.0261%
363/1,392,246 alleles · ultra-rare
exomes 360/1,242,738 · genomes 3/149,508 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.083% | 1,205 |
| Finnishnot grpmax-eligible | 0.0501% | 1,995 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0479% | 2,088 |
| Admixed American | 0.0443% | 2,258 |
| Remaining individualsnot grpmax-eligible | 0.041% | 2,439 |
| East Asian | 0.028% | 3,573 |
| Middle Eastern | 0.0208% | 4,806 |
| European (non-Finnish) | 0.0207% | 4,842 |
| African / African-American | 0.00611% | 16,363 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NOVA2
- Protein
- p.Ala324del
- Coding
- c.958GCC[4]
- MANE Select
- NM_002516
- dbSNP
- rs771592016
- Type
- Microsatellite
- Location
- chr19:45940370 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 65.60 · 2 PDB
Disease context
NOVA2-related disorder
Similar variants
- NOVA2 p.Ala324_Asn325insAla Likely benign ★ same residue
- NOVA2 p.Ser404fs Uncertain significance same condition
- NOVA2 p.Gly369fs Likely pathogenic ★ same condition
- NOVA2 p.Leu276fs Likely pathogenic ★ same condition
- NOVA2 p.Val237Ala Uncertain significance ★ ⚠ same condition
- NOVA2 p.Ala384= Likely benign same condition
- NOVA2 p.Ala385= Likely benign same condition
- NOVA2 p.Ala386= 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-ala324del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown