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

Gene ID: 344148, updated on 5-Mar-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, Apr 2022]
Expression
Broad expression in lung (RPKM 2.7), kidney (RPKM 0.7) and 20 other tissues See more
Orthologs
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Genomic context

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Location:
2q21.2
Exon count:
29
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (132671788..133674836, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (133110139..134114523, complement)
105.20220307 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. 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
  4. 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
  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 (26) 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)

Genotypes

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

Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
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 cellular_component ND
No biological Data available
more info
  
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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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_2023_10

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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