NPHP1 c.*17C>T
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000933%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.32 | GERP -2.8 |
| Non-coding constraint | Z 1.19 | 1 kb window · o/e 0.91 · regional · uncalibrated |
| Overall | ||
| CADD | 1.872 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000933%
European (non-Finnish) · 11/1,179,478 alleles
Filtering AF
0.0005%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000366%
Overall
0.000682%
11/1,612,838 alleles · very rare
exomes 10/1,460,688 · genomes 1/152,150 · 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.*17C>T
- MANE Select
- NM_001128178
- Type
- single nucleotide variant
- Location
- chr2:110123774 (GRCh38)
- Gene constraint
- LOEUF 0.92 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.22 · 2 PDB
Similar variants
- NPHP1 c.1083+1G>A Likely pathogenic ★★ same type
- NPHP1 c.1270-1G>A Pathogenic ★★ same type
- NPHP1 c.1270-2A>G Pathogenic/Likely pathogenic ★★ same type
- NPHP1 c.143+1G>C Likely pathogenic ★★ same type
- NPHP1 c.144-1G>A Pathogenic/Likely pathogenic ★★ same type
- NPHP1 c.1716+1G>T Pathogenic/Likely pathogenic ★★ same type
- NPHP1 c.329+1G>A Pathogenic/Likely pathogenic ★★ same type
- NPHP1 c.522+1G>A Likely pathogenic ★★ same type
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-star-17c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown