GANAB p.Val554=
c.1662C>T · rs1179948177 · VCV2049900
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 Δ0.86 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP -0.45, phastCons 1 |
| Overall | ||
| CADD | 7.715 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,016 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000616%
9/1,461,646 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,008 |
| East Asian | 0.00223% | 44,886 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,500 |
| African / African-American | 0.00133% | 75,052 |
| European (non-Finnish) | 0.000339% | 294,958 |
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.Val554=
- Coding
- c.1662C>T
- MANE Select
- NM_198334
- dbSNP
- rs1179948177
- Type
- single nucleotide variant
- Location
- chr11:62629889 (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.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-val554 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown