GAN p.Ala49=
c.147G>A · VCV4741613
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,572,994)
Conditions
1
giant axonal neuropathy 1
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 1.1 | GERP 0.29, phastCons 1 |
| Overall | ||
| CADD | 13.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,572,994). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- GAN
- Protein
- p.Ala49=
- Coding
- c.147G>A
- MANE Select
- NM_022041
- Type
- single nucleotide variant
- Location
- chr16:81315260 (GRCh38)
- Gene constraint
- LOEUF 0.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.93 · 2 PDB
- Residue 49
- the btb domain; an α-helix
Disease context
giant axonal neuropathy 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Giant axonal neuropathy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy
Similar variants
- GAN p.Ala49Glu Uncertain significance ⚠ same residue
- GAN p.Ala49Thr Uncertain significance ⚠ same residue
- GAN c.1502+1G>T Pathogenic/Likely pathogenic ★★ same condition
- GAN c.851+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GAN p.Arg545His Pathogenic/Likely pathogenic ★★ same condition
- GAN p.Gln103Ter Pathogenic ★★ same condition
- GAN p.Glu486Lys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GAN c.1373+4C>T Uncertain significance ★★ same condition
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/gan-p-ala49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown