ATL1 p.Val464=
c.1392G>C · rs2504578054 · VCV2103477
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hereditary spastic paraplegia 3A
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 3.5 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 8.002 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ATL1
- Protein
- p.Val464=
- Coding
- c.1392G>C
- MANE Select
- NM_015915
- dbSNP
- rs2504578054
- Type
- single nucleotide variant
- Location
- chr14:50628303 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.36 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 86.49 · 14 PDB
Disease context
hereditary spastic paraplegia 3A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal dominant spastic paraplegia type 3 (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult, Childhood
- Prevalence
- 1-9 / 1 000 000 (Portugal)
Similar variants
- ATL1 p.Val464Met Uncertain significance ★ ⚠ same residue
- ATL1 p.Arg217Gln Pathogenic/Likely pathogenic ★★ same condition
- ATL1 p.Arg239Cys Pathogenic/Likely pathogenic ★★ same condition
- ATL1 p.Arg239His Likely pathogenic ★★ same condition
- ATL1 p.Arg403Pro Likely pathogenic ★★ same condition
- ATL1 p.Arg415Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ATL1 p.Arg416Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ATL1 p.Arg495Trp Pathogenic/Likely pathogenic ★★ 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/atl1-p-val464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown