PSAP p.Ala39fs
c.116del · VCV4908001
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
PSAP-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 14 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.6 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- PSAP
- Protein
- p.Ala39fs
- Coding
- c.116del
- MANE Select
- NM_002778
- Type
- Deletion
- Location
- chr10:71834430 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 73.90 · 21 PDB
- Residue 39
- the saposin a-type 1 domain
Disease context
PSAP-related disorder
Similar variants
- PSAP p.Ala39= Likely benign ★ same residue
- PSAP p.Asn215His Pathogenic/Likely pathogenic ★★ same condition
- PSAP p.Met277Leu Uncertain significance ★ ⚠ same condition
- PSAP c.1432-29C>G Benign same condition
- PSAP c.-7C>G Likely benign same condition
- PSAP c.720+2_720+5del Likely pathogenic ★★ same type
- PSAP p.Lys227del Pathogenic/Likely pathogenic ★★ same type
- PSAP c.41-17_42del 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/psap-p-ala39fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown