GANAB p.Val82=
c.246C>T · rs189470436 · VCV1661514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0469%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.94 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 0.76, phastCons 1 |
| Overall | ||
| CADD | 9.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0469%
East Asian · 21/44,760 alleles
Filtering AF
0.0314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0263%
Overall
0.00206%
33/1,599,154 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0469% | 2,131 |
| South Asian | 0.00551% | 18,146 |
| Remaining individualsnot grpmax-eligible | 0.00484% | 20,654 |
| European (non-Finnish) | 0.000343% | 291,703 |
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
- GANAB
- Protein
- p.Val82=
- Coding
- c.246C>T
- MANE Select
- NM_198334
- dbSNP
- rs189470436
- Type
- single nucleotide variant
- Location
- chr11:62639365 (GRCh38)
- Gene constraint
- LOEUF 0.391 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.43 · 2 PDB
- Residue 82
- a turn
Similar variants
- GANAB p.Arg112Ter Likely pathogenic ★★ same type
- GANAB p.Arg164Ter Pathogenic/Likely pathogenic ★★ same type
- GANAB p.Arg61Ter Pathogenic ★★ same type
- GANAB p.Arg812Ter Pathogenic/Likely pathogenic ★★ same type
- GANAB p.Arg815Ter Pathogenic/Likely pathogenic ★★ same type
- GANAB p.Arg817Trp Likely pathogenic ★★ same type
- GANAB p.Gln414Ter Pathogenic/Likely pathogenic ★★ same type
- GANAB p.Gln837Ter Pathogenic/Likely pathogenic ★★ 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/ganab-p-val82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown