CEP164 p.Ser519fs
c.1556del · VCV4723880
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
nephronophthisis 15
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 13 of 33 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -3.3 | GERP -3.1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CEP164
- Protein
- p.Ser519fs
- Coding
- c.1556del
- MANE Select
- NM_014956
- Type
- Deletion
- Location
- chr11:117381847 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.08 · 4 PDB
- Residue 519
- the 'disordered' region
Disease context
nephronophthisis 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Senior-Loken syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- CEP164 p.Arg897fs Pathogenic/Likely pathogenic ★★ same condition
- CEP164 p.Glu704fs Pathogenic/Likely pathogenic ★★ same condition
- CEP164 p.Glu745fs Likely pathogenic ★★ same condition
- CEP164 p.Leu433fs Pathogenic/Likely pathogenic ★★ same condition
- CEP164 p.Trp1336fs Pathogenic/Likely pathogenic ★★ same condition
- CEP164 c.3278+5_3278+8del Uncertain significance ★★ same condition
- CEP164 p.Glu745del Uncertain significance ★★ same condition
- CEP164 p.Gly215del Uncertain significance ★★ 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/cep164-p-ser519fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown