Q9UBB6 · NCDN_HUMAN

  • Protein
    Neurochondrin
  • Gene
    NCDN
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

function

Probably involved in signal transduction in the nervous system, via increasing cell surface localization of GRM5/mGluR5 and positively regulating its signaling (PubMed:33711248).
Required for the spatial learning process. Acts as a negative regulator of Ca2+-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth (Probable).

GO annotations

all annotationsall molecular functionvirus receptor activitydna bindingrna bindingcytoskeletal motor activitycatalytic activitygtpase activitystructural molecule activitytransporter activitycytoskeletal protein bindinglipid bindingcyclase activityantioxidant activityoxidoreductase activitytransferase activityhydrolase activitylyase activityisomerase activityligase activityprotein tag activitycargo receptor activityhistone bindingprotein folding chaperonetranslation regulator activitynutrient reservoir activityreceptor ligand activitymolecular transducer activitymolecular adaptor activitytoxin activitycell adhesion mediator activitymolecular function regulator activityvirus coreceptor activitycatalytic activity, acting on a proteincatalytic activity, acting on dnacatalytic activity, acting on rnamolecular carrier activitytranscription regulator activitygeneral transcription initiation factor activitymolecular sensor activitymolecular sequestering activityatp-dependent activityother molecular functionall biological processmitotic cell cyclecytokinesiscytoplasmic translationimmune system processmuscle system processcirculatory system processrenal system processrespiratory system processcarbohydrate metabolic processgeneration of precursor metabolites and energydna replicationdna repairdna recombinationchromatin organizationdna-templated transcriptionregulation of dna-templated transcriptiontrna metabolic processprotein foldingprotein glycosylationamino acid metabolic processmodified amino acid metabolic processlipid metabolic processvitamin metabolic processsulfur compound metabolic processintracellular protein transportnucleocytoplasmic transportautophagyinflammatory responsemitochondrion organizationcytoskeleton organizationmicrotubule-based movementperoxisome organizationlysosome organizationchromosome segregationcell adhesionestablishment or maintenance of cell polarityprogrammed cell deathphotosynthesismrna metabolic processsnrna metabolic processvesicle-mediated transportreproductive processdigestive system processsignalingcell differentiationprotein catabolic processextracellular matrix organizationregulatory ncrna-mediated gene silencingtelomere organizationcell junction organizationwound healingribosome biogenesiscilium organizationanatomical structure developmentcell motilitynervous system processendocrine processprotein maturationtransmembrane transportnucleobase-containing small molecule metabolic processhepaticobiliary system processmembrane organizationprotein-containing complex assemblycell wall organization or biogenesisnitrogen cycle metabolic processprotein localization to plasma membranedefense response to other organismdetoxificationmeiotic nuclear divisionmitotic nuclear divisionmitochondrial gene expressioncarbohydrate derivative metabolic processother biological processall cellular componentnuclear chromosomeextracellular regionextracellular spacecell wallnucleusnuclear envelopenucleoplasmchromosomenucleolusmitochondrionlysosomeendosomevacuoleperoxisomeendoplasmic reticulumgolgi apparatuslipid dropletmicrotubule organizing centercytosolribosomecytoskeletonplasma membraneciliumplastidthylakoidexternal encapsulating structureextracellular matrixcytoplasmic vesicleorganelleother cellular component
Cell color indicative of number of GO terms
AspectTerm
Cellular Componentcytosol
Cellular Componentdendrite
Cellular Componentendosome membrane
Cellular Componentmembrane
Cellular Componentneuronal cell body
Cellular Componentperikaryon
Cellular Componentpostsynapse
Biological Processbone resorption
Biological Processneuron projection development
Biological Processregulation of neuronal synaptic plasticity

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Neurochondrin

Gene names

    • Name
      NCDN
    • Synonyms
      KIAA0607

Organism names

  • Taxonomic identifier
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo

Accessions

  • Primary accession
    Q9UBB6
  • Secondary accessions
    • D3DPR9
    • Q9UBY2
    • Q9Y4A6
    • Q9Y4D9

Proteomes

Organism-specific databases

Subcellular Location

Cytoplasm, cytosol
Endosome membrane
; Lipid-anchor
Postsynapse
Note: Localizes to somatic regions of neurons. Localization to endosome membrane requires palmitoylation.

Keywords

Disease & Variants

Involvement in disease

Neurodevelopmental disorder with infantile epileptic spasms (NEDIES)

  • Note
    • The disease is caused by variants affecting the gene represented in this entry
  • Description
    An autosomal dominant neurodevelopmental disorder characterized by onset of severe and frequent epileptic spasms within the first year of life. Affected individuals have global developmental delay with delayed walking and poor or absent speech. More variable features may include poor overall growth, high-arched palate, and delayed myelination on brain imaging.
  • See also
    MIM:619373
Natural variants in NEDIES
Variant IDPosition(s)ChangeDescription
VAR_085876433E>Qin NEDIES; uncertain significance; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; no effect on phosphorylation of ERK1/ERK2
VAR_085877478R>Qin NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; no effect on phosphorylation of ERK1/ERK2
VAR_085878498W>Rin NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; in these cells, there is markedly decreased phosphorylation of ERK1/ERK2, compared to wild-type, suggesting impaired GRM5 activation
VAR_085879652P>Lin NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; in these cells, there is markedly decreased phosphorylation of ERK1/ERK2, compared to wild-type, suggesting impaired GRM5 activation

Features

Showing features for natural variant.

TypeIDPosition(s)Description
Natural variantVAR_039849392in a colorectal cancer sample; somatic mutation; dbSNP:rs753974779
Natural variantVAR_039850392in a colorectal cancer sample; somatic mutation
Natural variantVAR_085876433in NEDIES; uncertain significance; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; no effect on phosphorylation of ERK1/ERK2
Natural variantVAR_085877478in NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; no effect on phosphorylation of ERK1/ERK2
Natural variantVAR_085878498in NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; in these cells, there is markedly decreased phosphorylation of ERK1/ERK2, compared to wild-type, suggesting impaired GRM5 activation
Natural variantVAR_085879652in NEDIES; in the neuroblastoma cell line SH-SY5Y, in which NCDN has been knocked out, does not rescue impaired neurite formation following retinoic acid treatment, contrary to wild-type; in these cells, there is markedly decreased phosphorylation of ERK1/ERK2, compared to wild-type, suggesting impaired GRM5 activation

Variants

We now provide the "Disease & Variants" viewer in its own tab.

The viewer provides 647 variants from UniProt as well as other sources including ClinVar and dbSNP.

Go to variant viewer

Keywords

Organism-specific databases

Miscellaneous

Genetic variation databases

PTM/Processing

Features

Showing features for initiator methionine, modified residue, modified residue (large scale data), chain, lipidation.

TypeIDPosition(s)SourceDescription
Initiator methionine1UniProtRemoved
Initiator methionine1UniProtIn isoform Q9UBB6-2; Removed
Modified residue2UniProtN-acetylserine
Modified residue2UniProtPhosphoserine
Modified residue2UniProtIn isoform Q9UBB6-2; N-acetylalanine
Modified residue (large scale data)2PRIDEPhosphoserine
ChainPRO_00003246172-729UniProtNeurochondrin
Lipidation3UniProtS-palmitoyl cysteine
Lipidation4UniProtS-palmitoyl cysteine
Modified residue (large scale data)20PRIDEPhosphoserine
Modified residue75UniProtAsymmetric dimethylarginine
Modified residue448UniProtPhosphoserine
Modified residue (large scale data)448PRIDEPhosphoserine
Modified residue (large scale data)582PRIDEPhosphothreonine
Modified residue (large scale data)583PRIDEPhosphoserine

Post-translational modification

Palmitoylated. Palmitoylation by ZDHHC1, ZDHHC3 and ZDHHC11 regulates the association of NCDN with endosome membranes. May also be palmitoylated by ZDHHC7.

Keywords

Proteomic databases

PTM databases

Expression

Tissue specificity

Abundantly expressed in whole adult brain and in all individual brain regions examined, including spinal cord. Weakly expressed in ovary, testis, fetal brain and small intestine.

Gene expression databases

Organism-specific databases

Interaction

Subunit

Interacts with MCHR1 (PubMed:16945926).
Interacts with SEMA4C (By similarity).
Interacts with DIAPH1 (via FH3 domain) (By similarity).
Interacts with GRM5 (By similarity).

Binary interactions

Protein-protein interaction databases

Miscellaneous

Structure

Family & Domains

Sequence similarities

Belongs to the neurochondrin family.

Phylogenomic databases

Family and domain databases

Sequence & Isoform

Align isoforms (2)
  • Sequence status
    Complete

This entry describes 2 isoforms produced by Alternative splicing.

Q9UBB6-1

This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

  • Name
    1
  • Synonyms
    NCDN1, Neurochondrin-1
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Length
    729
  • Mass (Da)
    78,864
  • Last updated
    2000-05-01 v1
  • Checksum
    FA8D46B06CE1F5AB
MSCCDLAAAGQLGKASIMASDCEPALNQAEGRNPTLERYLGALREAKNDSEQFAALLLVTKAVKAGDIDAKTRRRIFDAVGFTFPNRLLTTKEAPDGCPDHVLRALGVALLACFCSDPELAAHPQVLNKIPILSTFLTARGDPDDAARRSMIDDTYQCLTAVAGTPRGPRHLIAGGTVSALCQAYLGHGYGFDQALALLVGLLAAAETQCWKEAEPDLLAVLRGLSEDFQKAEDASKFELCQLLPLFLPPTTVPPECYRDLQAGLARILGSKLSSWQRNPALKLAARLAHACGSDWIPAGSSGSKFLALLVNLACVEVRLALEETGTEVKEDVVTACYALMELGIQECTRCEQSLLKEPQKVQLVSVMKEAIGAVIHYLLQVGSEKQKEPFVFASVRILGAWLAEETSSLRKEVCQLLPFLVRYAKTLYEEAEEANDLSQQVANLAISPTTPGPTWPGDALRLLLPGWCHLTVEDGPREILIKEGAPSLLCKYFLQQWELTSPGHDTSVLPDSVEIGLQTCCHIFLNLVVTAPGLIKRDACFTSLMNTLMTSLPALVQQQGRLLLAANVATLGLLMARLLSTSPALQGTPASRGFFAAAILFLSQSHVARATPGSDQAVLALSPEYEGIWADLQELWFLGMQAFTGCVPLLPWLAPAALRSRWPQELLQLLGSVSPNSVKPEMVAAYQGVLVELARANRLCREAMRLQAGEETASHYRMAALEQCLSEP

Q9UBB6-2

  • Name
    2
  • Synonyms
    NCDN2, Neurochondrin-2
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Computationally mapped potential isoform sequences

There are 2 potential isoforms mapped to this entry

View all
EntryEntry nameGene nameLength
C9J5H8C9J5H8_HUMANNCDN244
H7C2R2H7C2R2_HUMANNCDN193

Sequence caution

The sequence AAD05029.1 differs from that shown. Reason: Erroneous gene model prediction
The sequence BAA25533.1 differs from that shown. Reason: Erroneous initiation Extended N-terminus.

Features

Showing features for alternative sequence.

TypeIDPosition(s)Description
Alternative sequenceVSP_0323151-17in isoform 2

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AB018739
EMBL· GenBank· DDBJ
BAA85384.2
EMBL· GenBank· DDBJ
mRNA
AB018740
EMBL· GenBank· DDBJ
BAA85385.2
EMBL· GenBank· DDBJ
mRNA
AB027514
EMBL· GenBank· DDBJ
BAA77830.1
EMBL· GenBank· DDBJ
Genomic DNA
AB027514
EMBL· GenBank· DDBJ
BAA77831.1
EMBL· GenBank· DDBJ
Genomic DNA
AB011179
EMBL· GenBank· DDBJ
BAA25533.1
EMBL· GenBank· DDBJ
mRNA Different initiation
AC004865
EMBL· GenBank· DDBJ
AAD05029.1
EMBL· GenBank· DDBJ
Genomic DNA Sequence problems.
CH471059
EMBL· GenBank· DDBJ
EAX07410.1
EMBL· GenBank· DDBJ
Genomic DNA
CH471059
EMBL· GenBank· DDBJ
EAX07411.1
EMBL· GenBank· DDBJ
Genomic DNA
CH471059
EMBL· GenBank· DDBJ
EAX07412.1
EMBL· GenBank· DDBJ
Genomic DNA
BC024592
EMBL· GenBank· DDBJ
AAH24592.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

Disclaimer

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