CSPP1 c.-56del
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000932%, nfe)
Conditions
1
Joubert syndrome 21
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 -1.5 | GERP -2.1 |
| Non-coding constraint | Z 2.07 | 1 kb window · o/e 0.85 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000932%
European (non-Finnish) · 11/1,179,858 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000753%
11/1,461,484 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
- CSPP1
- Coding
- c.-56del
- MANE Select
- NM_001382391
- dbSNP
- rs762868036
- Type
- Deletion
- Location
- chr8:67064490 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 57.34
Similar variants
- CSPP1 c.-54_-51del Likely pathogenic ★★ same condition
- CSPP1 p.Asn908fs Pathogenic ★★ same condition
- CSPP1 p.Gln753fs Pathogenic/Likely pathogenic ★★ same condition
- CSPP1 p.Glu11fs Pathogenic/Likely pathogenic ★★ same condition
- CSPP1 p.Glu755fs Pathogenic ★★ same condition
- CSPP1 p.Glu89fs Pathogenic ★★ same condition
- CSPP1 p.His85fs Pathogenic ★★ same condition
- CSPP1 p.Ile841fs 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/cspp1-c-minus-56del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown