NPHP1 p.Arg541=
c.1623G>A · rs2467168372 · VCV2093301
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
nephronophthisis
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 -0.065 | GERP -1.9 |
| Overall | ||
| CADD | 8.027 | 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
- NPHP1
- Protein
- p.Arg541=
- Coding
- c.1623G>A
- MANE Select
- NM_001128178
- dbSNP
- rs2467168372
- Type
- single nucleotide variant
- Location
- chr2:110131698 (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 p.Arg541Gly Uncertain significance ★ ⚠ same residue
- 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
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-p-arg541 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown