GANAB p.Asp699=
c.2097T>C · VCV3685040
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
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 -0.79 | GERP 1 |
| Overall | ||
| CADD | 5.461 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,614,122 alleles · very rare
exomes 1/1,461,864 · genomes 0/152,258 · joint denominator
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.Asp699=
- Coding
- c.2097T>C
- MANE Select
- NM_198334
- Type
- single nucleotide variant
- Location
- chr11:62628852 (GRCh38)
- Gene constraint
- LOEUF 0.391 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.43 · 2 PDB
- Residue 699
- an α-helix
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-asp699 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown