NOVA2 p.Gly31=
c.93C>T · VCV4536711
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00268%, afr)
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 -0.85 | GERP -5.3 |
| Overall | ||
| CADD | 5.245 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
African / African-American · 2/74,744 alleles
Filtering AF
0.000444%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.00025%
4/1,598,952 alleles · very rare
exomes 3/1,446,908 · genomes 1/152,044 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00268% | 37,372 |
| European (non-Finnish) | 0.00017% | 586,607 |
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.Gly31=
- Coding
- c.93C>T
- MANE Select
- NM_002516
- Type
- single nucleotide variant
- Location
- chr19:45961146 (GRCh38)
- Gene constraint
- LOEUF 0.611 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 65.60 · 2 PDB
Similar variants
- NOVA2 p.Gly31Ala Uncertain significance ★ ⚠ same residue
- NOVA2 p.Ala247Thr Uncertain significance ★★ ⚠ same type
- NOVA2 p.Ala287= Benign ★★ same type
- NOVA2 p.Ala383= Benign/Likely benign ★★ same type
- NOVA2 p.Asn292Thr Likely benign ★★ same type
- NOVA2 p.Ile39= Benign/Likely benign ★★ same type
- NOVA2 p.Leu135= Likely benign ★★ same type
- NOVA2 p.Leu238= Benign ★★ same type
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-gly31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown