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NPHP4 nephrocystin 4 [ Homo sapiens (human) ]

Gene ID: 261734, updated on 5-Mar-2024

Summary

Official Symbol
NPHP4provided by HGNC
Official Full Name
nephrocystin 4provided by HGNC
Primary source
HGNC:HGNC:19104
See related
Ensembl:ENSG00000131697 MIM:607215; AllianceGenome:HGNC:19104
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
POC10; SLSN4
Summary
This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal disease, and with Senior-Loken syndrome type 4, a combination of nephronophthisis and retinitis pigmentosa. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2014]
Expression
Broad expression in testis (RPKM 3.4), thyroid (RPKM 2.6) and 25 other tissues See more
Orthologs
NEW
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Try the new Transcript table

Genomic context

See NPHP4 in Genome Data Viewer
Location:
1p36.31
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (5862811..5992425, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (5387041..5518608, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (5922871..6052485, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903830 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5778898-5779859 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:5800808-5801308 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:5801309-5801809 Neighboring gene AJAP1-NPHP4 intergenic nontranscribed DNase I hypersensitive site-defined enhancer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5805858-5806654 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5814163-5814801 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:5815304-5815502 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5826901-5827548 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:5827549-5828196 and GRCh37_chr1:5828197-5828844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5857583-5858292 Neighboring gene NANOG hESC enhancer GRCh37_chr1:5883532-5884116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5886314-5886814 Neighboring gene Sharpr-MPRA regulatory region 9093 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5891751-5892261 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:5896941-5897093 Neighboring gene MPRA-validated peak24 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5910393-5910894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5910895-5911394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5913107-5913951 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5917575-5918327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5918328-5919080 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5939868-5940372 Neighboring gene microRNA 4689 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5956455-5957256 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:5957257-5958056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5968773-5969298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5979954-5980454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:5999651-6000151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6004026-6004526 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6009504-6009801 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6027103-6027602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6031677-6032176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6051054-6051908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 70 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6059331-6060045 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6060046-6060760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6062904-6063618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6068670-6069262 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6070973-6071474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6072741-6073242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6084854-6085618 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 71 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:6086382-6087145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 74 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 73 Neighboring gene potassium voltage-gated channel subfamily A regulatory beta subunit 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6113495-6113995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6120127-6120627 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:6133526-6134725 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:6143081-6143561 Neighboring gene uncharacterized LOC124903831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162189-6162690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6162691-6163190 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 137 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6186229-6187116 Neighboring gene Sharpr-MPRA regulatory region 11871 Neighboring gene chromodomain helicase DNA binding protein 5 Neighboring gene MPRA-validated peak27 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6225727-6226227 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6238637-6239138 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:6239139-6239638

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Nephronophthisis 4 Compare labs
Senior-Loken syndrome 4
MedGen: C1846979 OMIM: 606996 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Common variants at ten loci influence QT interval duration in the QTGEN Study.
EBI GWAS Catalog
Genetic association with overall survival of taxane-treated lung cancer patients - A genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ46306, KIAA0673

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables structural molecule activity NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
 
located_in cell-cell junction IDA
Inferred from Direct Assay
more info
PubMed 
located_in centriole IEA
Inferred from Electronic Annotation
more info
 
located_in centrosome IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in ciliary basal body IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in ciliary base IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in ciliary transition zone IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in non-motile cilium IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in photoreceptor distal connecting cilium IEA
Inferred from Electronic Annotation
more info
 
located_in ribbon synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
nephrocystin-4
Names
POC10 centriolar protein homolog
nephroretinin

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011724.2 RefSeqGene

    Range
    5047..134661
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291593.2NP_001278522.1  nephrocystin-4 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks three exons and uses an alternate splice site in the 5' region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (b) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK124074, AK314326
    UniProtKB/TrEMBL
    B3KW36
  2. NM_001291594.2NP_001278523.1  nephrocystin-4 isoform c

    See identical proteins and their annotated locations for NP_001278523.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks four exons in the 5' region, and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK124074, AK314326, BC040520
    UniProtKB/TrEMBL
    B3KW36
    Related
    ENST00000478423.6
  3. NM_015102.5NP_055917.1  nephrocystin-4 isoform a

    See identical proteins and their annotated locations for NP_055917.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF537130, AK314326, BU738621, R40620
    Consensus CDS
    CCDS44052.1
    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
    Related
    ENSP00000367398.4, ENST00000378156.9

RNA

  1. NR_111987.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains three alternate internal exons and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL356693, BC040520, R40620
    Related
    ENST00000489180.6

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    5862811..5992425 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710563.4XP_006710626.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_006710626.1

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  2. XM_017000999.2XP_016856488.1  nephrocystin-4 isoform X10

  3. XM_047417537.1XP_047273493.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  4. XM_047417599.1XP_047273555.1  nephrocystin-4 isoform X10

  5. XM_047417546.1XP_047273502.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  6. XM_047417538.1XP_047273494.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  7. XM_047417590.1XP_047273546.1  nephrocystin-4 isoform X10

  8. XM_011541217.3XP_011539519.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_011539519.1

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  9. XM_047417589.1XP_047273545.1  nephrocystin-4 isoform X10

  10. XM_047417535.1XP_047273491.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  11. XM_047417581.1XP_047273537.1  nephrocystin-4 isoform X10

  12. XM_011541216.3XP_011539518.1  nephrocystin-4 isoform X5

    See identical proteins and their annotated locations for XP_011539518.1

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  13. XM_047417585.1XP_047273541.1  nephrocystin-4 isoform X10

  14. XM_047417593.1XP_047273549.1  nephrocystin-4 isoform X10

  15. XM_011541215.2XP_011539517.1  nephrocystin-4 isoform X4

  16. XM_047417565.1XP_047273521.1  nephrocystin-4 isoform X7

  17. XM_017000996.2XP_016856485.1  nephrocystin-4 isoform X3

  18. XM_011541213.2XP_011539515.1  nephrocystin-4 isoform X1

  19. XM_047417555.1XP_047273511.1  nephrocystin-4 isoform X6

  20. XM_011541214.2XP_011539516.1  nephrocystin-4 isoform X2

  21. XM_017001000.3XP_016856489.1  nephrocystin-4 isoform X10

  22. XM_047417607.1XP_047273563.1  nephrocystin-4 isoform X12

  23. XM_017001001.2XP_016856490.1  nephrocystin-4 isoform X11

  24. XM_047417574.1XP_047273530.1  nephrocystin-4 isoform X8

  25. XM_017000998.1XP_016856487.1  nephrocystin-4 isoform X9

  26. XM_017001002.2XP_016856491.1  nephrocystin-4 isoform X13

    Related
    ENSP00000481831.2, ENST00000622020.4
  27. XM_047417617.1XP_047273573.1  nephrocystin-4 isoform X14

RNA

  1. XR_007058632.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    5387041..5518608 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335923.1XP_054191898.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  2. XM_054335933.1XP_054191908.1  nephrocystin-4 isoform X10

  3. XM_054335921.1XP_054191896.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  4. XM_054335931.1XP_054191906.1  nephrocystin-4 isoform X10

  5. XM_054335929.1XP_054191904.1  nephrocystin-4 isoform X10

  6. XM_054335924.1XP_054191899.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  7. XM_054335920.1XP_054191895.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  8. XM_054335919.1XP_054191894.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  9. XM_054335917.1XP_054191892.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  10. XM_054335918.1XP_054191893.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  11. XM_054335932.1XP_054191907.1  nephrocystin-4 isoform X10

  12. XM_054335930.1XP_054191905.1  nephrocystin-4 isoform X10

  13. XM_054335922.1XP_054191897.1  nephrocystin-4 isoform X5

    UniProtKB/Swiss-Prot
    O75161, Q8IWC0
  14. XM_054335916.1XP_054191891.1  nephrocystin-4 isoform X4

  15. XM_054335926.1XP_054191901.1  nephrocystin-4 isoform X7

  16. XM_054335915.1XP_054191890.1  nephrocystin-4 isoform X3

  17. XM_054335913.1XP_054191888.1  nephrocystin-4 isoform X1

  18. XM_054335925.1XP_054191900.1  nephrocystin-4 isoform X6

  19. XM_054335914.1XP_054191889.1  nephrocystin-4 isoform X2

  20. XM_054335934.1XP_054191909.1  nephrocystin-4 isoform X10

  21. XM_054335936.1XP_054191911.1  nephrocystin-4 isoform X12

  22. XM_054335935.1XP_054191910.1  nephrocystin-4 isoform X11

  23. XM_054335927.1XP_054191902.1  nephrocystin-4 isoform X8

  24. XM_054335928.1XP_054191903.1  nephrocystin-4 isoform X9

  25. XM_054335937.1XP_054191912.1  nephrocystin-4 isoform X13

  26. XM_054335938.1XP_054191913.1  nephrocystin-4 isoform X14

RNA

  1. XR_008485989.1 RNA Sequence