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    NKD2 NKD inhibitor of WNT signaling pathway 2 [ Homo sapiens (human) ]

    Gene ID: 85409, updated on 9-Jun-2024

    Summary

    Official Symbol
    NKD2provided by HGNC
    Official Full Name
    NKD inhibitor of WNT signaling pathway 2provided by HGNC
    Primary source
    HGNC:HGNC:17046
    See related
    Ensembl:ENSG00000145506 MIM:607852; AllianceGenome:HGNC:17046
    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
    Naked2
    Summary
    This gene encodes a member of a family of proteins that function as negative regulators of Wnt receptor signaling through interaction with Dishevelled family members. The encoded protein participates in the delivery of transforming growth factor alpha-containing vesicles to the cell membrane. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012]
    Expression
    Broad expression in lung (RPKM 6.0), skin (RPKM 2.9) and 15 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NKD2 in Genome Data Viewer
    Location:
    5p15.33
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (1008802..1038943)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (914423..943101)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (1008917..1039058)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:991246-991960 Neighboring gene long intergenic non-protein coding RNA 2982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:994888-995388 Neighboring gene uncharacterized LOC124900932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1004327-1004970 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1004971-1005615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1005616-1006259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1007413-1008178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1008179-1008944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1017054-1017554 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1018687-1019370 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1022097-1022758 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:1024745-1025404 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1025625-1026127 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1026128-1026629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1026630-1027132 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1028355-1028856 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1038746-1039520 Neighboring gene solute carrier family 12 member 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1067605-1068104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1068827-1069326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1073082-1073636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1073637-1074191 Neighboring gene microRNA 4635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1099659-1100505 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1100506-1101352 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:1106433-1107278 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:1117531-1118064 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:1119135-1119668 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1128375-1128908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1129443-1129976 Neighboring gene uncharacterized LOC107986396 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:1131579-1132112

    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

    EBI GWAS Catalog

    Description
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATPase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables growth factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables molecular adaptor activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables myosin heavy chain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cell periphery IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in exocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    protein naked cuticle homolog 2
    Names
    Dvl-binding protein NKD2
    NKD2, WNT signaling pathway inhibitor
    naked cuticle homolog 2

    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.

    mRNA and Protein(s)

    1. NM_001271082.2NP_001258011.1  protein naked cuticle homolog 2 isoform 2

      See identical proteins and their annotated locations for NP_001258011.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC116351
      Consensus CDS
      CCDS59486.1
      UniProtKB/Swiss-Prot
      Q969F2
      Related
      ENSP00000274150.4, ENST00000274150.4
    2. NM_033120.4NP_149111.1  protein naked cuticle homolog 2 isoform 1

      See identical proteins and their annotated locations for NP_149111.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC116351
      Consensus CDS
      CCDS3859.1
      UniProtKB/Swiss-Prot
      Q969F2, Q96EK8, Q9BSN0
      Related
      ENSP00000296849.5, ENST00000296849.10

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      1008802..1038943
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248382.4XP_005248439.1  protein naked cuticle homolog 2 isoform X1

      See identical proteins and their annotated locations for XP_005248439.1

    2. XM_011514150.4XP_011512452.1  protein naked cuticle homolog 2 isoform X2

      See identical proteins and their annotated locations for XP_011512452.1

    3. XM_005248383.5XP_005248440.1  protein naked cuticle homolog 2 isoform X3

      See identical proteins and their annotated locations for XP_005248440.1

    4. XM_017010000.2XP_016865489.1  protein naked cuticle homolog 2 isoform X4

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187548.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      27309..57450
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328665.1XP_054184640.1  protein naked cuticle homolog 2 isoform X1

    2. XM_054328666.1XP_054184641.1  protein naked cuticle homolog 2 isoform X2

    3. XM_054328667.1XP_054184642.1  protein naked cuticle homolog 2 isoform X3

    4. XM_054328668.1XP_054184643.1  protein naked cuticle homolog 2 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      914423..943101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353728.1XP_054209703.1  protein naked cuticle homolog 2 isoform X1

    2. XM_054353729.1XP_054209704.1  protein naked cuticle homolog 2 isoform X2

    3. XM_054353730.1XP_054209705.1  protein naked cuticle homolog 2 isoform X3

    4. XM_054353731.1XP_054209706.1  protein naked cuticle homolog 2 isoform X4