NPHP3 p.Leu1072=
c.3216T>A · VCV3344267
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
NPHP3-related disorder
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 -0.63 | GERP -3.6 |
| Overall | ||
| CADD | 0.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NPHP3
- Protein
- p.Leu1072=
- Coding
- c.3216T>A
- MANE Select
- NM_153240
- Type
- single nucleotide variant
- Location
- chr3:132686373 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.59 · 1 PDB
Similar variants
- NPHP3 p.Leu1072Phe Uncertain significance ★ ⚠ same residue
- NPHP3 c.823+1G>T Likely pathogenic ★★ same condition
- NPHP3 p.Arg142Ter Pathogenic/Likely pathogenic ★★ same condition
- NPHP3 p.Arg577Ter Pathogenic ★★ same condition
- NPHP3 p.Arg702Ter Pathogenic ★★ same condition
- NPHP3 p.Gln1136Ter Pathogenic ★★ same condition
- NPHP3 p.Glu461Ter Pathogenic ★★ same condition
- NPHP3 p.Gly935= Pathogenic/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/nphp3-p-leu1072 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown