GANAB p.Asp474=
c.1422C>T · VCV3626392
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00263%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.26 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 5.639 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00263%
European (non-Finnish) · 31/1,180,038 alleles
Filtering AF
0.00188%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00164%
Overall
0.00198%
32/1,614,044 alleles · very rare
exomes 31/1,461,838 · genomes 1/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00263% | 38,066 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Asp474=
- Coding
- c.1422C>T
- MANE Select
- NM_198334
- Type
- single nucleotide variant
- Location
- chr11:62630470 (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.Asp474Tyr 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-asp474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown