AP5Z1 p.Ser244=
c.732T>C · rs2115109498 · VCV1933634
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 48
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 0.1 | GERP -2.6, phastCons 0.92 |
| Overall | ||
| CADD | 6.611 | 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
- AP5Z1
- Protein
- p.Ser244=
- Coding
- c.732T>C
- MANE Select
- NM_014855
- dbSNP
- rs2115109498
- Type
- single nucleotide variant
- Location
- chr7:4784313 (GRCh38)
- Gene constraint
- LOEUF 1.641 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.32
Disease context
hereditary spastic paraplegia 48 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Autosomal recessive spastic paraplegia type 48 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adult
Similar variants
- AP5Z1 p.Ser244Cys Uncertain significance ★★ ⚠ same residue
- AP5Z1 c.1312-2A>G Pathogenic/Likely pathogenic ★★ same condition
- AP5Z1 c.1707+1G>A Likely pathogenic ★★ same condition
- AP5Z1 c.1806-1G>C Likely pathogenic ★★ same condition
- AP5Z1 p.Arg138Ter Pathogenic/Likely pathogenic ★★ same condition
- AP5Z1 p.Arg310Ter Pathogenic/Likely pathogenic ★★ same condition
- AP5Z1 p.Arg311Ter Pathogenic/Likely pathogenic ★★ same condition
- AP5Z1 p.Arg345Ter 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/ap5z1-p-ser244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown