NPHP3 c.1118+8del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000101%, nfe)
Conditions
1
nephronophthisis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.4 | GERP -0.62, phastCons 0.23 |
| Non-coding constraint | Z 0.38 | 1 kb window · o/e 0.97 · regional · uncalibrated |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000101%
European (non-Finnish) · 1/987,194 alleles
Overall
7.27e-05%
1/1,374,900 alleles · very rare
exomes 1/1,222,588 · genomes 0/152,312 · 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
- NPHP3
- Coding
- c.1118+8del
- MANE Select
- NM_153240
- dbSNP
- rs2530483482
- Type
- Deletion
- Location
- chr3:132713118 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.59 · 1 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
- NPHP3 p.Arg157fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 p.Glu90_Tyr91insTer Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 p.His559fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 p.Phe1001fs Pathogenic ★★ same condition
- NPHP3 p.Thr136fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 p.Val363fs Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 c.3697-11_3697-7del Uncertain significance ★★ same condition
- NPHP3 c.1118+17del Likely benign ★★ 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/nphp3-c-1118-plus-8del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown