Q9UBB6 · NCDN_HUMAN
- ProteinNeurochondrin
- GeneNCDN
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids729 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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 annotations | all molecular function | virus receptor activity | dna binding | rna binding | cytoskeletal motor activity | catalytic activity | gtpase activity | structural molecule activity | transporter activity | cytoskeletal protein binding | lipid binding | cyclase activity | antioxidant activity | oxidoreductase activity | transferase activity | hydrolase activity | lyase activity | isomerase activity | ligase activity | protein tag activity | cargo receptor activity | histone binding | protein folding chaperone | translation regulator activity | nutrient reservoir activity | receptor ligand activity | molecular transducer activity | molecular adaptor activity | toxin activity | cell adhesion mediator activity | molecular function regulator activity | virus coreceptor activity | catalytic activity, acting on a protein | catalytic activity, acting on dna | catalytic activity, acting on rna | molecular carrier activity | transcription regulator activity | general transcription initiation factor activity | molecular sensor activity | molecular sequestering activity | atp-dependent activity | other molecular function | all biological process | mitotic cell cycle | cytokinesis | cytoplasmic translation | immune system process | muscle system process | circulatory system process | renal system process | respiratory system process | carbohydrate metabolic process | generation of precursor metabolites and energy | dna replication | dna repair | dna recombination | chromatin organization | dna-templated transcription | regulation of dna-templated transcription | trna metabolic process | protein folding | protein glycosylation | amino acid metabolic process | modified amino acid metabolic process | lipid metabolic process | vitamin metabolic process | sulfur compound metabolic process | intracellular protein transport | nucleocytoplasmic transport | autophagy | inflammatory response | mitochondrion organization | cytoskeleton organization | microtubule-based movement | peroxisome organization | lysosome organization | chromosome segregation | cell adhesion | establishment or maintenance of cell polarity | programmed cell death | photosynthesis | mrna metabolic process | snrna metabolic process | vesicle-mediated transport | reproductive process | digestive system process | signaling | cell differentiation | protein catabolic process | extracellular matrix organization | regulatory ncrna-mediated gene silencing | telomere organization | cell junction organization | wound healing | ribosome biogenesis | cilium organization | anatomical structure development | cell motility | nervous system process | endocrine process | protein maturation | transmembrane transport | nucleobase-containing small molecule metabolic process | hepaticobiliary system process | membrane organization | protein-containing complex assembly | cell wall organization or biogenesis | nitrogen cycle metabolic process | protein localization to plasma membrane | defense response to other organism | detoxification | meiotic nuclear division | mitotic nuclear division | mitochondrial gene expression | carbohydrate derivative metabolic process | other biological process | all cellular component | nuclear chromosome | extracellular region | extracellular space | cell wall | nucleus | nuclear envelope | nucleoplasm | chromosome | nucleolus | mitochondrion | lysosome | endosome | vacuole | peroxisome | endoplasmic reticulum | golgi apparatus | lipid droplet | microtubule organizing center | cytosol | ribosome | cytoskeleton | plasma membrane | cilium | plastid | thylakoid | external encapsulating structure | extracellular matrix | cytoplasmic vesicle | organelle | other cellular component | |||
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Aspect | Term | |
---|---|---|
Cellular Component | cytosol | |
Cellular Component | dendrite | |
Cellular Component | endosome membrane | |
Cellular Component | membrane | |
Cellular Component | neuronal cell body | |
Cellular Component | perikaryon | |
Cellular Component | postsynapse | |
Biological Process | bone resorption | |
Biological Process | neuron projection development | |
Biological Process | regulation of neuronal synaptic plasticity |
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameNeurochondrin
Gene names
Organism names
- Organism
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Primates > Haplorrhini > Catarrhini > Hominidae > Homo
Accessions
- Primary accessionQ9UBB6
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
UniProt Annotation
GO Annotation
Endosome membrane ; Lipid-anchor
Note: Localizes to somatic regions of neurons. Localization to endosome membrane requires palmitoylation.
Keywords
- Cellular component
Disease & Variants
Involvement in disease
Neurodevelopmental disorder with infantile epileptic spasms (NEDIES)
- Note
- DescriptionAn 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 alsoMIM:619373
Natural variants in NEDIES
Variant ID | Position(s) | Change | Description | |
---|---|---|---|---|
VAR_085876 | 433 | E>Q | in 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_085877 | 478 | R>Q | in 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_085878 | 498 | W>R | in 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_085879 | 652 | P>L | in 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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Natural variant | VAR_039849 | 392 | in a colorectal cancer sample; somatic mutation; dbSNP:rs753974779 | |||
Sequence: V → E | ||||||
Natural variant | VAR_039850 | 392 | in a colorectal cancer sample; somatic mutation | |||
Sequence: V → L | ||||||
Natural variant | VAR_085876 | 433 | in 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 | |||
Sequence: E → Q | ||||||
Natural variant | VAR_085877 | 478 | in 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 | |||
Sequence: R → Q | ||||||
Natural variant | VAR_085878 | 498 | in 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 | |||
Sequence: W → R | ||||||
Natural variant | VAR_085879 | 652 | in 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 | |||
Sequence: P → L |
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.
Keywords
- Disease
Organism-specific databases
Miscellaneous
Genetic variation databases
PTM/Processing
Features
Showing features for initiator methionine, modified residue, modified residue (large scale data), chain, lipidation.
Type | ID | Position(s) | Source | Description | |||
---|---|---|---|---|---|---|---|
Initiator methionine | 1 | UniProt | Removed | ||||
Sequence: M | |||||||
Initiator methionine | 1 | UniProt | In isoform Q9UBB6-2; Removed | ||||
Sequence: M | |||||||
Modified residue | 2 | UniProt | N-acetylserine | ||||
Sequence: S | |||||||
Modified residue | 2 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 2 | UniProt | In isoform Q9UBB6-2; N-acetylalanine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 2 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Chain | PRO_0000324617 | 2-729 | UniProt | Neurochondrin | |||
Sequence: SCCDLAAAGQLGKASIMASDCEPALNQAEGRNPTLERYLGALREAKNDSEQFAALLLVTKAVKAGDIDAKTRRRIFDAVGFTFPNRLLTTKEAPDGCPDHVLRALGVALLACFCSDPELAAHPQVLNKIPILSTFLTARGDPDDAARRSMIDDTYQCLTAVAGTPRGPRHLIAGGTVSALCQAYLGHGYGFDQALALLVGLLAAAETQCWKEAEPDLLAVLRGLSEDFQKAEDASKFELCQLLPLFLPPTTVPPECYRDLQAGLARILGSKLSSWQRNPALKLAARLAHACGSDWIPAGSSGSKFLALLVNLACVEVRLALEETGTEVKEDVVTACYALMELGIQECTRCEQSLLKEPQKVQLVSVMKEAIGAVIHYLLQVGSEKQKEPFVFASVRILGAWLAEETSSLRKEVCQLLPFLVRYAKTLYEEAEEANDLSQQVANLAISPTTPGPTWPGDALRLLLPGWCHLTVEDGPREILIKEGAPSLLCKYFLQQWELTSPGHDTSVLPDSVEIGLQTCCHIFLNLVVTAPGLIKRDACFTSLMNTLMTSLPALVQQQGRLLLAANVATLGLLMARLLSTSPALQGTPASRGFFAAAILFLSQSHVARATPGSDQAVLALSPEYEGIWADLQELWFLGMQAFTGCVPLLPWLAPAALRSRWPQELLQLLGSVSPNSVKPEMVAAYQGVLVELARANRLCREAMRLQAGEETASHYRMAALEQCLSEP | |||||||
Lipidation | 3 | UniProt | S-palmitoyl cysteine | ||||
Sequence: C | |||||||
Lipidation | 4 | UniProt | S-palmitoyl cysteine | ||||
Sequence: C | |||||||
Modified residue (large scale data) | 20 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue | 75 | UniProt | Asymmetric dimethylarginine | ||||
Sequence: R | |||||||
Modified residue | 448 | UniProt | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 448 | PRIDE | Phosphoserine | ||||
Sequence: S | |||||||
Modified residue (large scale data) | 582 | PRIDE | Phosphothreonine | ||||
Sequence: T | |||||||
Modified residue (large scale data) | 583 | PRIDE | Phosphoserine | ||||
Sequence: S |
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
- PTM
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).
Interacts with SEMA4C (By similarity).
Interacts with DIAPH1 (via FH3 domain) (By similarity).
Interacts with GRM5 (By similarity).
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q9UBB6 | EFHC2 Q5JST6 | 6 | EBI-1053490, EBI-2349927 | |
BINARY | Q9UBB6 | KRT75 O95678 | 3 | EBI-1053490, EBI-2949715 | |
BINARY | Q9UBB6 | PAX6 P26367 | 3 | EBI-1053490, EBI-747278 | |
BINARY | Q9UBB6 | TINF2 Q9BSI4 | 2 | EBI-1053490, EBI-717399 | |
BINARY | Q9UBB6 | TLE5 Q08117 | 3 | EBI-1053490, EBI-717810 | |
BINARY | Q9UBB6 | ZBED1 O96006 | 3 | EBI-1053490, EBI-740037 | |
BINARY | Q9UBB6 | ZNF398 Q8TD17 | 3 | EBI-1053490, EBI-8643207 |
Protein-protein interaction databases
Miscellaneous
Structure
Sequence & Isoform
- Sequence statusComplete
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.
- Name1
- SynonymsNCDN1, Neurochondrin-1
- Length729
- Mass (Da)78,864
- Last updated2000-05-01 v1
- ChecksumFA8D46B06CE1F5AB
Q9UBB6-2
- Name2
- SynonymsNCDN2, Neurochondrin-2
- Differences from canonical
- 1-17: Missing
Computationally mapped potential isoform sequences
There are 2 potential isoforms mapped to this entry
Sequence caution
Features
Showing features for alternative sequence.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Alternative sequence | VSP_032315 | 1-17 | in isoform 2 | |||
Sequence: Missing |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |