PPT1 c.799del
Likely pathogenic
Multiple submitters
Classification
Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Conditions
1
neuronal ceroid lipofuscinosis 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 2.3, phastCons 1 |
| Non-coding constraint | Z 1.29 | 1 kb window · o/e 0.86 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,024 alleles
Overall
6.84e-05%
1/1,461,840 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PPT1
- Coding
- c.799del
- MANE Select
- NM_000310
- dbSNP
- rs1648444864
- Type
- Deletion
- Location
- chr1:40074183 (GRCh38)
- Gene constraint
- LOEUF 0.733 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.05 · 1 PDB
Disease context
neuronal ceroid lipofuscinosis 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor CLN1 disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- PPT1 p.Cys152fs Pathogenic/Likely pathogenic ★★ same condition
- PPT1 p.Glu59fs Pathogenic ★★ same condition
- PPT1 p.Gly270_Leu271insTer Pathogenic/Likely pathogenic ★★ same condition
- PPT1 p.Leu10fs Pathogenic/Likely pathogenic ★★ same condition
- PPT1 p.Met133fs Pathogenic/Likely pathogenic ★★ same condition
- PPT1 p.Ser3fs Pathogenic/Likely pathogenic ★★ same condition
- PPT1 c.433+7_433+8del Likely benign ★★ same condition
- PPT1 c.124+1215_235-103del 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/ppt1-c-799del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown