Is NPHP3 p.Cys302fs (c.905del) pathogenic?

NPHP3 p.Cys302fs (c.905del) is classified Likely pathogenic in NPHP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-01-31). Associated with NPHP3-related disorder.

What condition is associated with NPHP3 p.Cys302fs (c.905del)?

NPHP3 p.Cys302fs (c.905del) is associated with NPHP3-related disorder (ClinVar).

NPHP3 p.Cys302fs

c.905del · VCV4964300

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

NPHP3-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 5 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 0.83, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: NPHP3
Protein: p.Cys302fs
Coding: c.905del
MANE Select: NM_153240
Type: Deletion
Location: chr3:132715137 (GRCh38)
Gene constraint: LOEUF 0.873 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.59 · 1 PDB

Full NPHP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

NPHP3-related disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NPHP3 c.3570+1del Likely pathogenic ★★ same condition
NPHP3 p.Glu90_Tyr91insTer Pathogenic/Likely pathogenic ★★ same condition
NPHP3 p.Met491fs Pathogenic/Likely pathogenic ★★ same condition
NPHP3 p.Thr136fs Pathogenic/Likely pathogenic ★★ same condition
NPHP3 p.His883fs Likely pathogenic ★ same condition
NPHP3 p.Leu539fs Likely pathogenic ★ same condition
NPHP3 p.Ser906fs Likely pathogenic ★ same condition
NPHP3 p.Leu1078fs 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-cys302fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown