NPHP4 p.Lys36fs
c.107del · VCV3587248
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
nephronophthisis 4
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 2 of 30 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 4.7 | GERP 0.98, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NPHP4
- Protein
- p.Lys36fs
- Coding
- c.107del
- MANE Select
- NM_015102
- Type
- Deletion
- Location
- chr1:5986183 (GRCh38)
- Gene constraint
- LOEUF 1.183 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.44
Disease context
nephronophthisis 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: Senior-Loken syndrome 4
For Nephronophthisis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Finland)
Similar variants
- NPHP4 c.3817-12_3818del Likely pathogenic ★★ same condition
- NPHP4 p.Ala279fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Ala565fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Gln1050fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Gly1028fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Gly529fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Lys424fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP4 p.Phe63fs 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/nphp4-p-lys36fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown