NPHP3 c.1275+12del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
nephronophthisis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +12 | near-intronic (+12 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -0.036 |
| Non-coding constraint | Z 1.02 | 1 kb window · o/e 0.92 · regional · uncalibrated |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- NPHP3
- Coding
- c.1275+12del
- MANE Select
- NM_153240
- dbSNP
- rs2107990515
- Type
- Deletion
- Location
- chr3:132708089 (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-1275-plus-12del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown