NPHP1 c.69+18del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
nephronophthisis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +18 | near-intronic (+18 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1 | GERP 0.77 |
| Non-coding constraint | Z -0.45 | 1 kb window · o/e 1.03 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,028 alleles
Overall
6.2e-05%
1/1,613,414 alleles · very rare
exomes 1/1,461,066 · genomes 0/152,348 · joint denominator
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
- NPHP1
- Coding
- c.69+18del
- MANE Select
- NM_001128178
- dbSNP
- rs1165664417
- Type
- Deletion
- Location
- chr2:110204882 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.22 · 2 PDB
Disease context
nephronophthisis — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Nephronophthisis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Finland)
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-c-69-plus-18del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown