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NCDN neurochondrin [ Homo sapiens (human) ]

Gene ID: 23154, updated on 5-Mar-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (35557799..35566779)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (35420844..35429828)
105.20220307 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
  • 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. 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
  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. Molecular cloning and expression of human neurochondrin-1 and -2. Mochizuki R, et al. Biochim Biophys Acta, 1999 Sep 3. PMID 10524216
  4. Altered Norbin Expression in Patients with Epilepsy and a Rat Model. Xu Y, et al. Sci Rep, 2017 Oct 25. PMID 29070854, Free PMC Article
  5. Neurochondrin is an atypical RIIα-specific A-kinase anchoring protein. Hermann JS, et al. Biochim Biophys Acta, 2015 Oct. PMID 25916936, Free PMC Article

See all (57) 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
  
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 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_2023_10

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

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