NPHP1 p.Asn293fs
c.878del · VCV3584257
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
3
nephronophthisis 1
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 10 of 20 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.8 | GERP -1.2, phastCons 0.97 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NPHP1
- Protein
- p.Asn293fs
- Coding
- c.878del
- MANE Select
- NM_001128178
- Type
- Deletion
- Location
- chr2:110161679 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.22 · 2 PDB
Similar variants
- NPHP1 c.141_143+40del Likely pathogenic ★★ same condition
- NPHP1 p.Asn61fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 p.Asp162fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 p.Glu454fs Pathogenic ★★ same condition
- NPHP1 p.Ile517fs Pathogenic ★★ same condition
- NPHP1 p.Lys185fs Pathogenic ★★ same condition
- NPHP1 p.Lys377fs Pathogenic ★★ same condition
- NPHP1 p.Ser129fs 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/nphp1-p-asn293fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown