VPS13A p.Pro1255fs
c.3761dup · rs2131376583 · VCV1451324
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 33 of 72 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.93 | GERP -4, phastCons 0.003 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. 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
- VPS13A
- Protein
- p.Pro1255fs
- Coding
- c.3761dup
- MANE Select
- NM_033305
- dbSNP
- rs2131376583
- Type
- Duplication
- Location
- chr9:77295790 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1255
- a UniProt-annotated variant site (in chac)
Similar variants
- VPS13A c.187+1dup Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Ala969fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Asp1483fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Cys1979fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Glu3131fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Leu1289fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Leu782fs Pathogenic/Likely pathogenic ★★ same type
- VPS13A p.Ser1416fs 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/vps13a-p-pro1255fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown