ALPL c.997+1del
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Rare
Conditions
1
hypophosphatasia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 6.2 | GERP 0.67, phastCons 1 |
| Non-coding constraint | Z 2.45 | 1 kb window · o/e 0.83 · regional · uncalibrated |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ALPL
- Coding
- c.997+1del
- MANE Select
- NM_000478
- Type
- Deletion
- Location
- chr1:21573799 (GRCh38)
- Gene constraint
- LOEUF 0.987 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.74 · 5 PDB
Disease context
hypophosphatasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hypophosphatasia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- All ages
Similar variants
- ALPL c.793-30_793-11del Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Ala492fs Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Arg138fs Pathogenic ★★ same condition
- ALPL p.Arg272fs Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Asn16fs Pathogenic ★★ same condition
- ALPL p.Asn190del Pathogenic/Likely pathogenic ★★ same condition
- ALPL p.Asn302fs Pathogenic ★★ same condition
- ALPL p.Gln143fs 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/alpl-c-997-plus-1del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown