GANAB p.Val25=
c.75C>G · rs113618920 · VCV780996
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.76%, 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 1.2 | GERP -1.5, phastCons 1 |
| Overall | ||
| CADD | 3.587 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.76%
African / African-American · 3,568/74,964 alleles
Filtering AF
4.63%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.58%
Overall
0.245%
3,946/1,613,892 alleles · low-frequency
exomes 1,915/1,461,694 · genomes 2,031/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.76% | 21 |
| Remaining individualsnot grpmax-eligible | 0.277% | 361 |
| Admixed American | 0.262% | 382 |
| Middle Eastern | 0.132% | 758 |
| South Asian | 0.00878% | 11,385 |
| European (non-Finnish) | 0.00271% | 36,871 |
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.Val25=
- Coding
- c.75C>G
- MANE Select
- NM_198334
- dbSNP
- rs113618920
- Type
- single nucleotide variant
- Location
- chr11:62639695 (GRCh38)
- Gene constraint
- LOEUF 0.391 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 93.43 · 2 PDB
Similar variants
- GANAB p.Val25Ile Uncertain significance ★ ⚠ same residue
- 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
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-val25 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown