CSPP1 p.Glu824fs
c.2463_2469dup · rs863225191 · VCV217643
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 6.701e-06)
Conditions
1
Joubert syndrome 21
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 21 of 31 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.5, phastCons 1 |
| Region caveats | ||
| Repeat context | tandem | (GAAGAAA)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.00067%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- CSPP1
- Protein
- p.Glu824fs
- Coding
- c.2463_2469dup
- MANE Select
- NM_001382391
- dbSNP
- rs863225191
- Type
- Microsatellite
- Location
- chr8:67159049 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 57.34
- Residue 824
- the 'disordered' region
Similar variants
- CSPP1 p.Glu822fs Pathogenic/Likely pathogenic ★★ same condition
- CSPP1 p.Lys819fs Pathogenic ★★ same condition
- CSPP1 c.2392-8_2392-4del Benign/Likely benign ★★ same condition
- CSPP1 p.Arg761fs Pathogenic ★ same condition
- CSPP1 p.Asn515fs Pathogenic ★ same condition
- CSPP1 p.Glu204delinsIleTer Pathogenic ★ same condition
- CSPP1 p.Lys619fs Pathogenic ★ same condition
- CSPP1 p.Lys791fs 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-p-glu824fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown