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    NCDN neurochondrin [ Homo sapiens (human) ]

    Gene ID: 23154, updated on 28-Oct-2024

    Summary

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    Official Symbol
    NCDNprovided by HGNC
    Official Full Name
    neurochondrinprovided by HGNC
    Primary source
    HGNC:HGNC:17597
    See related
    Ensembl:ENSG00000020129 MIM:608458; AllianceGenome:HGNC:17597
    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
    NEDIES
    Summary
    This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 97.7), adrenal (RPKM 7.8) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NCDN in Genome Data Viewer
    Location:
    1p34.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (35557799..35566779)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35420844..35429828)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36023400..36032380)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene KIAA0319 like Neighboring gene RNY5 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35916701-35916880 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 728 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:35931229-35931375 Neighboring gene Sharpr-MPRA regulatory region 12145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 729 Neighboring gene zinc finger protein 485 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:35996497-35996998 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:35996999-35997498 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 731 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 640 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36019721-36020677 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36020678-36021633 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36022434-36023161 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36023162-36023888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 643 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36024616-36025341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36025798-36026432 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36035818-36035919 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36038879-36039378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36039620-36040366 Neighboring gene TFAP2E antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36042064-36042916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36042917-36043769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36055869-36056370 Neighboring gene transcription factor AP-2 epsilon Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36056371-36056870 Neighboring gene proteasome 20S subunit beta 2 Neighboring gene Sharpr-MPRA regulatory region 1763 Neighboring gene MPRA-validated peak173 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr1:36106102-36107067 and GRCh37_chr1:36107068-36108032

    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. Molecular cloning and expression of human neurochondrin-1 and -2. Mochizuki R, et al. Biochim Biophys Acta, 1999 Sep 3. PMID 10524216
    2. Corrigendum to 'Molecular cloning and expression of human neurochondrin-1 and -2'(1). Mochizuki R, et al. Biochim Biophys Acta, 2000 Feb 29. PMID 10684983
    3. Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy. Fatima A, et al. Am J Hum Genet, 2021 Apr 1. PMID 33711248, Free PMC Article
    4. Neurochondrin is an atypical RIIα-specific A-kinase anchoring protein. Hermann JS, et al. Biochim Biophys Acta, 2015 Oct. PMID 25916936, Free PMC Article
    5. Neurochondrin negatively regulates CaMKII phosphorylation, and nervous system-specific gene disruption results in epileptic seizure. Dateki M, et al. J Biol Chem, 2005 May 27. PMID 15790563

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.
      Title: Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.
    2. Low norbin expression is associated with Epilepsy.
      Title: Altered Norbin Expression in Patients with Epilepsy and a Rat Model.
    3. Schizophrenia subjects compared to controls showed a marked increase in CA1 hippocampal Norbin, and Tamalin proteins (47% and 34% respectively), which are endogenous regulators of mGluR5 signalling and trafficking
      Title: Metabotropic glutamate receptor 5, and its trafficking molecules Norbin and Tamalin, are increased in the CA1 hippocampal region of subjects with schizophrenia.
    4. we demonstrate that neurochondrin has strong isoform selectivity towards the RIIa subunit of PKA with nanomolar affinity
      Title: Neurochondrin is an atypical RIIα-specific A-kinase anchoring protein.
    5. In silico screening for palmitoyl substrates reveals a role for DHHC1/3/10 (zDHHC1/3/11)-mediated neurochondrin palmitoylation in its targeting to Rab5-positive endosomes.
      Title: In silico screening for palmitoyl substrates reveals a role for DHHC1/3/10 (zDHHC1/3/11)-mediated neurochondrin palmitoylation in its targeting to Rab5-positive endosomes.
    6. A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration.
      Title: Proteomic analysis identifies dysfunction in cellular transport, energy, and protein metabolism in different brain regions of atypical frontotemporal lobar degeneration.
    7. In mouse, the encoded protein is a negative regulator of Ca/calmodulin-dependent protein kinase II phosphorylation and is essential for the spatial learning process.
      Title: Neurochondrin negatively regulates CaMKII phosphorylation, and nervous system-specific gene disruption results in epileptic seizure.
    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
    Neurodevelopmental disorder with infantile epileptic spasms
    MedGen: C5543538 OMIM: 619373 GeneReviews: Not available
    		not available

    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

    Clone Names

    • KIAA0607

    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 bone resorption IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron projection development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of neuronal synaptic plasticity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of postsynaptic neurotransmitter receptor internalization IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    NOT located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuronal cell body ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    NOT located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    neurochondrin
    Names
    norbin

    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_001014839.2 → NP_001014839.1  neurochondrin isoform 1

      See identical proteins and their annotated locations for NP_001014839.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as NCDN-1, encodes the longer isoform (1).
      Source sequence(s)
      AB018739, AL536768, AW207151, BC024592
      Consensus CDS
      CCDS392.1
      UniProtKB/Swiss-Prot
      D3DPR9, Q9UBB6, Q9UBY2, Q9Y4A6, Q9Y4D9
      Related
      ENSP00000348394.4, ENST00000356090.8
      Conserved Domains (1) summary
      pfam05536
      Location:30 → 637
      Neurochondrin

    2. NM_001014841.2 → NP_001014841.1  neurochondrin isoform 2

      See identical proteins and their annotated locations for NP_001014841.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as NCDN-2, contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus when compared to isoform 1.
      Source sequence(s)
      AB018740, AL536768, AW207151, BC024592
      Consensus CDS
      CCDS30672.1
      UniProtKB/Swiss-Prot
      Q9UBB6
      Related
      ENSP00000362350.3, ENST00000373253.7
      Conserved Domains (1) summary
      pfam05536
      Location:13 → 620
      Neurochondrin

    3. NM_014284.3 → NP_055099.1  neurochondrin isoform 1

      See identical proteins and their annotated locations for NP_055099.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      AL536768, AW207151, BC024592, BI545092
      Consensus CDS
      CCDS392.1
      UniProtKB/Swiss-Prot
      D3DPR9, Q9UBB6, Q9UBY2, Q9Y4A6, Q9Y4D9
      Related
      ENSP00000362340.2, ENST00000373243.7
      Conserved Domains (1) summary
      pfam05536
      Location:30 → 637
      Neurochondrin

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      35557799..35566779
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      35420844..35429828
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UBB6.1 GenPept UniProtKB/Swiss-Prot:Q9UBB6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
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