NPHP1 c.771+30C>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
nephronophthisis
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| Splice region | donor +30 | near-intronic (+30 nt from the splice site) |
|---|---|---|
| SpliceAI | Δ0.29 | donor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 0.41 | GERP 0.16, phastCons 0.011 |
| Non-coding constraint | Z 0.26 | 1 kb window · o/e 0.98 · regional · uncalibrated |
| Overall | ||
| CADD | 14.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
6.2e-05%
1/1,613,904 alleles · ultra-rare
exomes 1/1,461,736 · genomes 0/152,168 · 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.771+30C>A
- MANE Select
- NM_001128178
- Type
- single nucleotide variant
- Location
- chr2:110164658 (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.1270-1G>A Pathogenic ★★ same condition
- NPHP1 c.1270-2A>G Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 c.143+1G>C Likely pathogenic ★★ same condition
- NPHP1 c.144-1G>A Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 c.1716+1G>T Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 c.329+1G>A Pathogenic/Likely pathogenic ★★ same condition
- NPHP1 c.522+1G>A Likely pathogenic ★★ same condition
- NPHP1 c.729-2A>G 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-771-plus-30c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown