Gene
NPHP4
nephrocystin 4
- HGNC 19104(opens in a new tab)
- Ensembl gene ENSG00000131697(opens in a new tab)
- NCBI Gene 261734(opens in a new tab)
Summary
- Cytogenetic location
- 1p36.31
- Coordinates
- Chromosome 1: 5,862,811–5,992,425 (GRCh38)
- Exons
- 30 exons across 129.6 kb
- Protein
- 1,426 amino acids
- Inheritance
- Autosomal recessive
- Also known as
- SLSN4, KIAA0673, POC10
- MANE Select transcript
- ENST00000378156.9NM_015102.5
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Read NPHP4, and the rest of your genome, with one test.
From $449Free shipping · Results in 6–8 weeks
Get my Genome TestCurated report relevant to this gene
Nephronophthisis and Senior-Løken Syndrome
- Senior-Løken SyndromeAutosomal recessive
A form of nephronophthisis combined with retinal degeneration that can cause early vision loss.
- 2 GenCC submitters rate it definitive or strong
What knowing changes
Knowing prompts referral for an eye examination alongside kidney monitoring.
- NephronophthisisAutosomal recessive
A recessively inherited kidney disease, caused by variants in NPHP1 and other cilia genes, in which progressive tubulointerstitial scarring leads to kidney failure, typically in the first three decades of life.
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
What knowing changes
Knowing allows regular kidney function monitoring, timely planning for dialysis or transplantation, and carrier testing for relatives.
Inheritance
- Autosomal recessive
- It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.
How NPHP4 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 5 kb of the gene's 129.6 kb; 4,281 of those bases code for the protein.
How a genome test reads NPHP4
141
positions in NPHP4 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 129.6 kb of NPHP4, introns included, not only the 5 kb of exons.
Traits linked to NPHP4
The Human Phenotype Ontology lists these as features of the rare conditions NPHP4 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the eye
- Abnormal retinal pigmentation
- Breakdown of light-sensitive cells in back of eye
- Visual impairment
- Progressive loss of vision
- Rod-cone dystrophy
- Clouding of the lens of the eye
- Lazy eye
- Marked vision impairment
Show 1 more trait
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). NPHP4 gene: nephrocystin 4. Retrieved 16 October 2026, from https://dantelabs.com/genes/nphp4
Dante Labs. NPHP4 gene: nephrocystin 4 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nphp4
One test. A lifetime of answers.
From $449Free shipping · Results in 6–8 weeks