NPHP3 p.Pro57=
c.171C>A · rs778581370 · VCV597246
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,511,602)
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 -0.47 | GERP -2.5, phastCons 0.026 |
| Overall | ||
| CADD | 6.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,511,602). 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
- Protein
- p.Pro57=
- Coding
- c.171C>A
- MANE Select
- NM_153240
- dbSNP
- rs778581370
- Type
- single nucleotide variant
- Location
- chr3:132722185 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.59 · 1 PDB
Similar variants
- NPHP3 c.1985+1G>A Pathogenic/Likely pathogenic ★★ same type
- NPHP3 c.3201+1G>T Likely pathogenic ★★ same type
- NPHP3 c.393+1G>C Likely pathogenic ★★ same type
- NPHP3 c.520-1G>T Pathogenic ★★ same type
- NPHP3 c.823+1G>T Likely pathogenic ★★ same type
- NPHP3 c.958-2A>G Pathogenic ★★ same type
- NPHP3 p.Arg1125Ter Pathogenic ★★ same type
- NPHP3 p.Arg1259Ter Pathogenic/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/nphp3-p-pro57 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown