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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
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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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