NPHP3

Chr 3

nephrocystin 3

Also known as: CFAP31, MKS7, NPH3, RHPD, RHPD1, SLSN3

NCBI Gene: 27031ENSG00000113971UniProt: Q7Z494

This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtNephronophthisis 3
UniProtRenal-hepatic-pancreatic dysplasia 1
UniProtMeckel syndrome 7

Clinical highlights

Gene-disease validity (ClinGen)
nephronophthisis · ARDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
13
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.65
LOEUF
LOF
Mechanism· G2P
📖
GeneReview available — NPHP3
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
0.65LOEUF
pLI 0.000
Z-score 4.10
OE 0.50 (0.38–0.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.86Z-score
OE missense 0.91 (0.85–0.97)
627 obs / 690.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.50 (0.38–0.65)
0≤0.351.4
Missense OE?0.91 (0.85–0.97)
0≤0.61.4
Synonymous OE?0.89
0≤1.21.6
LoF obs/exp: 38 / 76.7Missense obs/exp: 627 / 690.9Syn Z: 1.41

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

NPHP3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients