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    KATNIP katanin interacting protein [ Homo sapiens (human) ]

    Gene ID: 23247, updated on 2-Nov-2024

    Summary

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    Official Symbol
    KATNIPprovided by HGNC
    Official Full Name
    katanin interacting proteinprovided by HGNC
    Primary source
    HGNC:HGNC:29068
    See related
    Ensembl:ENSG00000047578 MIM:616650; AllianceGenome:HGNC:29068
    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
    JBTS26; KIAA0556
    Summary
    This gene encodes a novel, evolutionarily conserved, ciliary protein. In human hTERT-RPE1 cells, the protein is found at the base of cilia, decorating the ciliary axoneme, and enriched at the ciliary tip. The protein binds to microtubules in vitro and regulates their stability when it is overexpressed. A null mutation in this gene has been associated with Joubert syndrome, a recessive disorder that is characterized by a distinctive mid-hindbrain and cerebellar malformation and is also often associated with wider ciliopathy symptoms. Consistently, in a serum-starvation ciliogenesis assay, human fibroblast cells derived from patients with the mutation display a reduced number of ciliated cells with abnormally long cilia. [provided by RefSeq, Feb 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 9.1), testis (RPKM 6.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See KATNIP in Genome Data Viewer
    Location:
    16p12.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (27550144..27780344)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (27828904..28059341)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (27561465..27791665)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10627 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27460829-27461706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10630 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10632 Neighboring gene interleukin 21 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27482643-27483144 Neighboring gene IL21R antisense RNA 1 Neighboring gene general transcription factor IIIC subunit 1 Neighboring gene MPRA-validated peak2546 silencer Neighboring gene Sharpr-MPRA regulatory regions 5680 and 15498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10634 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:27644974-27645660 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27648141-27648641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27652441-27653082 Neighboring gene uncharacterized LOC107984874 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27711973-27712473 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27713579-27714080 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:27714081-27714580 Neighboring gene uncharacterized LOC100128079 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27735309-27735809 Neighboring gene uncharacterized LOC105371157 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10635 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:27780758-27781957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27782794-27783559 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27785796-27786296 Neighboring gene MPRA-validated peak2549 silencer Neighboring gene GSG1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27863495-27863996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:27878335-27878836 Neighboring gene RNA, U6 small nuclear 159, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr16:27960751-27960921 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:28004462-28005661 Neighboring gene RNA, U6 small nuclear 1241, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. Identification of a homozygous nonsense mutation in KIAA0556 in a consanguineous family displaying Joubert syndrome. Roosing S, et al. Hum Genet, 2016 Aug. PMID 27245168, Free PMC Article
    2. The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia. Turner JS, et al. Mol Cell Biol, 2023. PMID 37665596, Free PMC Article
    3. Co-occurrence of mutations in KIF7 and KIAA0556 in Joubert syndrome with ocular coloboma, pituitary malformation and growth hormone deficiency: a case report and literature review. Niceta M, et al. BMC Pediatr, 2020 Mar 12. PMID 32164589, Free PMC Article
    4. Overlap of polymicrogyria, hydrocephalus, and Joubert syndrome in a family with novel truncating mutations in ADGRG1/GPR56 and KIAA0556. Cauley ES, et al. Neurogenetics, 2019 May. PMID 30982090
    5. Pathogenic variants of DYNC2H1, KIAA0556, and PTPN11 associated with hypothalamic hamartoma. Fujita A, et al. Neurology, 2019 Jul 16. PMID 31197031

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia.
      Title: The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia.
    2. Co-occurrence of mutations in KIF7 and KIAA0556 in Joubert syndrome with ocular coloboma, pituitary malformation and growth hormone deficiency: a case report and literature review.
      Title: Co-occurrence of mutations in KIF7 and KIAA0556 in Joubert syndrome with ocular coloboma, pituitary malformation and growth hormone deficiency: a case report and literature review.
    3. homozygous truncating mutations in both ADGRG1/GPR56 and KIAA0556 are found in brothers displaying an overlap of polymicrogyria, hydrocephalus, and Joubert syndrome
      Title: Overlap of polymicrogyria, hydrocephalus, and Joubert syndrome in a family with novel truncating mutations in ADGRG1/GPR56 and KIAA0556.
    4. Pathogenic germline variants of KIAA0556 associated with hypothalamic hamartoma were found.
      Title: Pathogenic variants of DYNC2H1, KIAA0556, and PTPN11 associated with hypothalamic hamartoma.
    5. Whole exome sequencing in a multiplex consanguineous family from India revealed a KIAA0556 homozygous single base pair deletion mutation (c.4420del; p.Met1474Cysfs*11). Knockdown of the gene in zebrafish resulted in a ciliopathy phenotype, rescued by co-injection of wildtype cDNA
      Title: Identification of a homozygous nonsense mutation in KIAA0556 in a consanguineous family displaying Joubert syndrome.
    6. KIAA0556 mutation identified in patients with Joubert syndrome. KIAA0556 binds to microtubules, p60/p80 katanins and genetically interacts with ARL13B.
      Title: KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome.
    7. KIAA0056 (also known as mouse MGC31549) is a strong candidate gene for retinitis pigmentosa, RP22 (human 16p12.3-p12.1). Conclusion is based on a massive expression data set for mouse (103 strains in Genenetwork.org) and joint analysis of RetNet database.
      Title: Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Joubert syndrome 26
    MedGen: C4084843 OMIM: 616784 GeneReviews: Joubert Syndrome
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cerebrospinal fluid circulation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular space HDA PubMed 

    General protein information

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    Preferred Names
    katanin-interacting protein

    NCBI Reference Sequences (RefSeq)

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    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_046731.2 RefSeqGene

      Range
      5002..235202
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015202.5 → NP_056017.4  katanin-interacting protein

      Status: REVIEWED

      Source sequence(s)
      AC002551, AC008732, AC016597, AC025275, AC092330
      Consensus CDS
      CCDS32415.1
      UniProtKB/Swiss-Prot
      A7E2C2, O60303
      Related
      ENSP00000261588.4, ENST00000261588.10
      Conserved Domains (1) summary
      pfam14652
      Location:1214 → 1533
      DUF4457; Domain of unknown function (DUF4457)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      27550144..27780344
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255201.4 → XP_005255258.1  katanin-interacting protein isoform X1

      Conserved Domains (2) summary
      pfam14652
      Location:1275 → 1594
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:785 → 1004
      DUF4641; Domain of unknown function (DUF4641)

    2. XM_005255202.4 → XP_005255259.1  katanin-interacting protein isoform X2

      Conserved Domains (2) summary
      pfam14652
      Location:1257 → 1576
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:767 → 986
      DUF4641; Domain of unknown function (DUF4641)

    3. XM_011545775.3 → XP_011544077.1  katanin-interacting protein isoform X4

      Conserved Domains (2) summary
      pfam14652
      Location:1235 → 1554
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:745 → 964
      DUF4641; Domain of unknown function (DUF4641)

    4. XM_005255203.4 → XP_005255260.1  katanin-interacting protein isoform X5

      Conserved Domains (2) summary
      pfam14652
      Location:1232 → 1551
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:742 → 961
      DUF4641; Domain of unknown function (DUF4641)

    5. XM_017023085.2 → XP_016878574.1  katanin-interacting protein isoform X8

    6. XM_011545776.3 → XP_011544078.1  katanin-interacting protein isoform X6

      Conserved Domains (2) summary
      pfam14652
      Location:1231 → 1550
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:741 → 960
      DUF4641; Domain of unknown function (DUF4641)

    7. XM_024450216.2 → XP_024305984.1  katanin-interacting protein isoform X7

      Conserved Domains (1) summary
      pfam14652
      Location:1213 → 1532
      DUF4457; Domain of unknown function (DUF4457)

    8. XM_047433842.1 → XP_047289798.1  katanin-interacting protein isoform X9

    9. XM_006721025.4 → XP_006721088.1  katanin-interacting protein isoform X10

      Conserved Domains (2) summary
      pfam14652
      Location:1188 → 1507
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:698 → 917
      DUF4641; Domain of unknown function (DUF4641)

    10. XM_017023087.2 → XP_016878576.1  katanin-interacting protein isoform X11

    11. XM_047433843.1 → XP_047289799.1  katanin-interacting protein isoform X12

    12. XM_047433844.1 → XP_047289800.1  katanin-interacting protein isoform X13

    13. XM_011545774.3 → XP_011544076.1  katanin-interacting protein isoform X3

      See identical proteins and their annotated locations for XP_011544076.1

      Conserved Domains (2) summary
      pfam14652
      Location:1249 → 1568
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:759 → 978
      DUF4641; Domain of unknown function (DUF4641)

    14. XM_005255206.4 → XP_005255263.1  katanin-interacting protein isoform X14

      Conserved Domains (2) summary
      pfam14652
      Location:1040 → 1187
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:785 → 929
      DUF4641; Domain of unknown function (DUF4641)

    15. XM_047433846.1 → XP_047289802.1  katanin-interacting protein isoform X17

    16. XM_011545773.3 → XP_011544075.1  katanin-interacting protein isoform X3

      See identical proteins and their annotated locations for XP_011544075.1

      Conserved Domains (2) summary
      pfam14652
      Location:1249 → 1568
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:759 → 978
      DUF4641; Domain of unknown function (DUF4641)

    17. XM_047433845.1 → XP_047289801.1  katanin-interacting protein isoform X15

    18. XM_005255208.3 → XP_005255265.1  katanin-interacting protein isoform X16

      Conserved Domains (2) summary
      pfam14652
      Location:807 → 1126
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:317 → 555
      DUF4641; Domain of unknown function (DUF4641)

    19. XM_011545777.3 → XP_011544079.1  katanin-interacting protein isoform X18

      Conserved Domains (2) summary
      pfam14652
      Location:582 → 901
      DUF4457; Domain of unknown function (DUF4457)
      pfam15483
      Location:92 → 311
      DUF4641; Domain of unknown function (DUF4641)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      27828904..28059341
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379898.1 → XP_054235873.1  katanin-interacting protein isoform X1

    2. XM_054379899.1 → XP_054235874.1  katanin-interacting protein isoform X2

    3. XM_054379902.1 → XP_054235877.1  katanin-interacting protein isoform X4

    4. XM_054379903.1 → XP_054235878.1  katanin-interacting protein isoform X5

    5. XM_054379906.1 → XP_054235881.1  katanin-interacting protein isoform X8

    6. XM_054379904.1 → XP_054235879.1  katanin-interacting protein isoform X6

    7. XM_054379905.1 → XP_054235880.1  katanin-interacting protein isoform X7

    8. XM_054379907.1 → XP_054235882.1  katanin-interacting protein isoform X9

    9. XM_054379908.1 → XP_054235883.1  katanin-interacting protein isoform X10

    10. XM_054379909.1 → XP_054235884.1  katanin-interacting protein isoform X11

    11. XM_054379910.1 → XP_054235885.1  katanin-interacting protein isoform X12

    12. XM_054379911.1 → XP_054235886.1  katanin-interacting protein isoform X13

    13. XM_054379901.1 → XP_054235876.1  katanin-interacting protein isoform X3

    14. XM_054379912.1 → XP_054235887.1  katanin-interacting protein isoform X14

    15. XM_054379915.1 → XP_054235890.1  katanin-interacting protein isoform X17

    16. XM_054379900.1 → XP_054235875.1  katanin-interacting protein isoform X3

    17. XM_054379913.1 → XP_054235888.1  katanin-interacting protein isoform X15

    18. XM_054379914.1 → XP_054235889.1  katanin-interacting protein isoform X16

    19. XM_054379916.1 → XP_054235891.1  katanin-interacting protein isoform X18

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60303.4 GenPept UniProtKB/Swiss-Prot:O60303

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