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    NCKAP5 NCK associated protein 5 [ Homo sapiens (human) ]

    Gene ID: 344148, updated on 27-Nov-2024

    Summary

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    Official Symbol
    NCKAP5provided by HGNC
    Official Full Name
    NCK associated protein 5provided by HGNC
    Primary source
    HGNC:HGNC:29847
    See related
    Ensembl:ENSG00000176771 MIM:608789; AllianceGenome:HGNC:29847
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NAP5; ERIH1; ERIH2
    Summary
    Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in lung (RPKM 2.7), kidney (RPKM 0.7) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NCKAP5 in Genome Data Viewer
    Location:
    2q21.2
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (132671788..133674836, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (133110139..134114523, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (133429361..134326034, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene G protein-coupled receptor 39 Neighboring gene RN7SK pseudogene 103 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:133362908-133363464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:133426641-133427604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16540 Neighboring gene LY6/PLAUR domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 3189 Neighboring gene uncharacterized LOC112268439 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:133713724-133714923 Neighboring gene NCKAP5 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:133803163-133804362 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:133897156-133897670 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:133897671-133898183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:134023302-134023925 Neighboring gene NCKAP5 antisense RNA 2 Neighboring gene RNA, U6 small nuclear 579, pseudogene Neighboring gene NCKAP5 intron CAGE-defined mid-level expression enhancer Neighboring gene RN7SK pseudogene 154 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:134227836-134228352 Neighboring gene NANOG hESC enhancer GRCh37_chr2:134401501-134402008 Neighboring gene RN7SK pseudogene 93 Neighboring gene Sharpr-MPRA regulatory region 15675 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:134575595-134576794 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16541 Neighboring gene uncharacterized LOC105373627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16542 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:134742538-134743737 Neighboring gene uncharacterized LOC105373628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16543

    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
    • 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. A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma. Osman W, et al. Hum Mol Genet, 2012 Jun 15. PMID 22419738
    2. Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia. Khor SS, et al. PeerJ, 2013. PMID 23646285, Free PMC Article
    3. A novel ligand for an SH3 domain of the adaptor protein Nck bears an SH2 domain and nuclear signaling motifs. Matuoka K, et al. Biochem Biophys Res Commun, 1997 Oct 20. PMID 9344857
    4. Genome-wide association study of bipolar disorder in European American and African American individuals. Smith EN, et al. Mol Psychiatry, 2009 Aug. PMID 19488044, Free PMC Article
    5. A genome-wide association study of brain lesion distribution in multiple sclerosis. Gourraud PA, et al. Brain, 2013 Apr. PMID 23412934, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study of bipolar disorder in European American and African American individuals.
    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

    EBI GWAS Catalog

    Description
    A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma.
    EBI GWAS Catalog
    A genome-wide association study of brain lesion distribution in multiple sclerosis.
    EBI GWAS Catalog
    A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
    EBI GWAS Catalog
    Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    EBI GWAS Catalog
    Genome-wide association study of HLA-DQB1*06:02 negative essential hypersomnia.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34870

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in microtubule bundle formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in microtubule depolymerization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in microtubule plus-end IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    nck-associated protein 5
    Names
    NAP-5
    peripheral clock protein 2

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_207363.3 → NP_997246.2  nck-associated protein 5 isoform 1

      See identical proteins and their annotated locations for NP_997246.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).
      Source sequence(s)
      AC010974, AC011243, AK057980, AK092189, AK124659, AY946008, CA438539
      Consensus CDS
      CCDS46418.1
      UniProtKB/Swiss-Prot
      B8ZZL0, O14513, Q29SS9, Q29ST0, Q2NL90, Q6ZVE2, Q8NAS3
      Related
      ENSP00000387128.1, ENST00000409261.6
      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    2. NM_207481.4 → NP_997364.3  nck-associated protein 5 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks several segments in the coding region but maintains the reading frame, compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AC010974, AC011243, AK057980, AK092189, AK124659, AY946007, CA438539
      Consensus CDS
      CCDS46417.1
      UniProtKB/Swiss-Prot
      O14513
      Related
      ENSP00000386952.1, ENST00000409213.5
      Conserved Domains (2) summary
      pfam15246
      Location:365 → 457
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 123
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      132671788..133674836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017003975.3 → XP_016859464.1  nck-associated protein 5 isoform X1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    2. XM_011511100.4 → XP_011509402.1  nck-associated protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011509402.1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    3. XM_047444134.1 → XP_047300090.1  nck-associated protein 5 isoform X8

    4. XM_005263660.5 → XP_005263717.1  nck-associated protein 5 isoform X1

      See identical proteins and their annotated locations for XP_005263717.1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    5. XM_047444129.1 → XP_047300085.1  nck-associated protein 5 isoform X3

      UniProtKB/Swiss-Prot
      B8ZZL0, O14513, Q29SS9, Q29ST0, Q2NL90, Q6ZVE2, Q8NAS3

    6. XM_047444133.1 → XP_047300089.1  nck-associated protein 5 isoform X8

    7. XM_011511099.4 → XP_011509401.1  nck-associated protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011509401.1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    8. XM_005263659.5 → XP_005263716.1  nck-associated protein 5 isoform X1

      See identical proteins and their annotated locations for XP_005263716.1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    9. XM_017003979.3 → XP_016859468.1  nck-associated protein 5 isoform X7

    10. XM_011511097.4 → XP_011509399.1  nck-associated protein 5 isoform X1

      See identical proteins and their annotated locations for XP_011509399.1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    11. XM_017003974.1 → XP_016859463.1  nck-associated protein 5 isoform X1

      Conserved Domains (3) summary
      pfam07321
      Location:32 → 162
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1468 → 1776
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:32 → 158
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    12. XM_011511104.1 → XP_011509406.1  nck-associated protein 5 isoform X4

      See identical proteins and their annotated locations for XP_011509406.1

      Conserved Domains (2) summary
      pfam15246
      Location:1400 → 1708
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:2 → 90
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    13. XM_047444128.1 → XP_047300084.1  nck-associated protein 5 isoform X2

    14. XM_011511102.3 → XP_011509404.1  nck-associated protein 5 isoform X2

      See identical proteins and their annotated locations for XP_011509404.1

      Conserved Domains (3) summary
      pfam07321
      Location:7 → 137
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1443 → 1751
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:7 → 133
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    15. XM_017003977.3 → XP_016859466.1  nck-associated protein 5 isoform X2

      Conserved Domains (3) summary
      pfam07321
      Location:7 → 137
      YscO; Type III secretion protein YscO
      pfam15246
      Location:1443 → 1751
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:7 → 133
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    16. XM_011511105.2 → XP_011509407.1  nck-associated protein 5 isoform X4

      See identical proteins and their annotated locations for XP_011509407.1

      Conserved Domains (2) summary
      pfam15246
      Location:1400 → 1708
      NCKAP5; Nck-associated protein 5, Peripheral clock protein
      cl23720
      Location:2 → 90
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)

    17. XM_017003978.3 → XP_016859467.1  nck-associated protein 5 isoform X6

    18. XM_047444130.1 → XP_047300086.1  nck-associated protein 5 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      133110139..134114523 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341747.1 → XP_054197722.1  nck-associated protein 5 isoform X1

    2. XM_054341744.1 → XP_054197719.1  nck-associated protein 5 isoform X1

    3. XM_054341742.1 → XP_054197717.1  nck-associated protein 5 isoform X1

    4. XM_054341743.1 → XP_054197718.1  nck-associated protein 5 isoform X1

    5. XM_054341752.1 → XP_054197727.1  nck-associated protein 5 isoform X3

    6. XM_054341758.1 → XP_054197733.1  nck-associated protein 5 isoform X8

    7. XM_054341757.1 → XP_054197732.1  nck-associated protein 5 isoform X8

    8. XM_054341746.1 → XP_054197721.1  nck-associated protein 5 isoform X1

    9. XM_054341756.1 → XP_054197731.1  nck-associated protein 5 isoform X7

    10. XM_054341745.1 → XP_054197720.1  nck-associated protein 5 isoform X1

    11. XM_054341748.1 → XP_054197723.1  nck-associated protein 5 isoform X1

    12. XM_054341753.1 → XP_054197728.1  nck-associated protein 5 isoform X4

    13. XM_054341750.1 → XP_054197725.1  nck-associated protein 5 isoform X2

    14. XM_054341749.1 → XP_054197724.1  nck-associated protein 5 isoform X2

    15. XM_054341751.1 → XP_054197726.1  nck-associated protein 5 isoform X2

    16. XM_054341754.1 → XP_054197729.1  nck-associated protein 5 isoform X4

    17. XM_054341755.1 → XP_054197730.1  nck-associated protein 5 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14513.2 GenPept UniProtKB/Swiss-Prot:O14513

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