NCDN neurochondrin [Homo sapiens (human)] - Gene

Summary

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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Low norbin expression is associated with Epilepsy.
Title: Altered Norbin Expression in Patients with Epilepsy and a Rat Model.
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.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-74563 (e-PCR)
- UniSTS:7938

G09494 (e-PCR)
- UniSTS:26138

AU048745 (e-PCR)
- UniSTS:145195

A005T45 (e-PCR)
- UniSTS:8685

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 more info	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)

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
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
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