GENE REFERENCE / HGNC:7905

NPHP1

nephrocystin 1

protein-coding gene2q13Gene information

What does this gene do?

The NPHP1 gene provides instructions for making the nephrocystin-1 protein. This protein is thought to play a role in cell structures called cilia, which are microscopic, finger-like projections that stick out from the surface of cells. Cilia participate in signaling pathways that transmit information within and between cells and are important for the development and function of many types of cells and tissues. Nephrocystin-1 is found at the base of cilia in cells of the kidneys, respiratory tract, and the light-sensitive tissue at the back of the eye (the retina). Although the specific function of nephrocystin-1 is not well understood, it is thought to interact with a number of other proteins as part of a large protein complex that may be important for normal cilia function.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2014-09.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
nephronophthisis 1MONDO:0009728 · Evaluated 2021-01-27	Autosomal recessive	DefinitiveKidney Cystic and Ciliopathy Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,284
Submissions for variants in or overlapping this gene: 2,161
Submissions explicitly reporting this gene: 1,963
Alleles reported pathogenic / likely pathogenic: 174
VariationIDs with uncertain significance: 431
VariationIDs with conflicting classifications: 60

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about NPHP1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 174 alleles in NPHP1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in NPHP1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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