Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	23154
Gene name	Neurochondrin
Gene symbol	NCDN
Synonyms (NCBI Gene)	NEDIES
Chromosome	1
Chromosome location	1p34.3
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

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Show/Hide all (221)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023258	hsa-miR-122-5p	Microarray	17612493
MIRT049742	hsa-miR-92a-3p	CLASH	23622248
MIRT040919	hsa-miR-18a-3p	CLASH	23622248
MIRT039427	hsa-miR-421	CLASH	23622248
MIRT608917	hsa-miR-331-3p	HITS-CLIP	23313552
MIRT608916	hsa-miR-4281	HITS-CLIP	23313552
MIRT608915	hsa-miR-3911	HITS-CLIP	23313552
MIRT608914	hsa-miR-644a	HITS-CLIP	23313552
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	23313552
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	23313552
MIRT608911	hsa-miR-147a	HITS-CLIP	23313552
MIRT608910	hsa-miR-574-5p	HITS-CLIP	23313552
MIRT608917	hsa-miR-331-3p	HITS-CLIP	23824327
MIRT608916	hsa-miR-4281	HITS-CLIP	23824327
MIRT608915	hsa-miR-3911	HITS-CLIP	23824327
MIRT608914	hsa-miR-644a	HITS-CLIP	23824327
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	23824327
MIRT608911	hsa-miR-147a	HITS-CLIP	23824327
MIRT608910	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT608917	hsa-miR-331-3p	HITS-CLIP	24906430
MIRT608916	hsa-miR-4281	HITS-CLIP	24906430
MIRT608915	hsa-miR-3911	HITS-CLIP	24906430
MIRT608914	hsa-miR-644a	HITS-CLIP	24906430
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	24906430
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	24906430
MIRT608911	hsa-miR-147a	HITS-CLIP	24906430
MIRT608910	hsa-miR-574-5p	HITS-CLIP	24906430
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	27418678
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	27418678
MIRT608911	hsa-miR-147a	HITS-CLIP	27418678
MIRT608911	hsa-miR-147a	HITS-CLIP	27418678
MIRT608917	hsa-miR-331-3p	HITS-CLIP	27418678
MIRT608915	hsa-miR-3911	HITS-CLIP	27418678
MIRT608915	hsa-miR-3911	HITS-CLIP	27418678
MIRT608916	hsa-miR-4281	HITS-CLIP	27418678
MIRT608916	hsa-miR-4281	HITS-CLIP	27418678
MIRT608910	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT608910	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT608910	hsa-miR-574-5p	HITS-CLIP	27418678
MIRT608914	hsa-miR-644a	HITS-CLIP	27418678
MIRT608914	hsa-miR-644a	HITS-CLIP	27418678
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	27418678
MIRT608917	hsa-miR-331-3p	HITS-CLIP	23313552
MIRT608916	hsa-miR-4281	HITS-CLIP	23313552
MIRT608915	hsa-miR-3911	HITS-CLIP	23313552
MIRT608914	hsa-miR-644a	HITS-CLIP	23313552
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	23313552
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	23313552
MIRT608911	hsa-miR-147a	HITS-CLIP	23313552
MIRT608910	hsa-miR-574-5p	HITS-CLIP	23313552
MIRT608917	hsa-miR-331-3p	HITS-CLIP	23824327
MIRT608916	hsa-miR-4281	HITS-CLIP	23824327
MIRT608915	hsa-miR-3911	HITS-CLIP	23824327
MIRT608914	hsa-miR-644a	HITS-CLIP	23824327
MIRT608913	hsa-miR-6867-5p	HITS-CLIP	23824327
MIRT608912	hsa-miR-133a-3p	HITS-CLIP	23824327
MIRT608911	hsa-miR-147a	HITS-CLIP	23824327
MIRT608910	hsa-miR-574-5p	HITS-CLIP	23824327
MIRT1176128	hsa-miR-103b	CLIP-seq
MIRT1176129	hsa-miR-1184	CLIP-seq
MIRT1176130	hsa-miR-1202	CLIP-seq
MIRT1176131	hsa-miR-1205	CLIP-seq
MIRT1176132	hsa-miR-1207-5p	CLIP-seq
MIRT1176133	hsa-miR-122	CLIP-seq
MIRT1176134	hsa-miR-1275	CLIP-seq
MIRT1176135	hsa-miR-1287	CLIP-seq
MIRT1176136	hsa-miR-140-3p	CLIP-seq
MIRT1176137	hsa-miR-147	CLIP-seq
MIRT1176138	hsa-miR-1587	CLIP-seq
MIRT1176139	hsa-miR-1827	CLIP-seq
MIRT1176140	hsa-miR-1909	CLIP-seq
MIRT1176141	hsa-miR-196a	CLIP-seq
MIRT1176142	hsa-miR-196b	CLIP-seq
MIRT1176143	hsa-miR-1976	CLIP-seq
MIRT1176144	hsa-miR-2052	CLIP-seq
MIRT1176145	hsa-miR-2110	CLIP-seq
MIRT1176146	hsa-miR-2114	CLIP-seq
MIRT1176147	hsa-miR-2467-3p	CLIP-seq
MIRT1176148	hsa-miR-2682	CLIP-seq
MIRT1176149	hsa-miR-3127-5p	CLIP-seq
MIRT1176150	hsa-miR-3135b	CLIP-seq
MIRT1176151	hsa-miR-3150a-3p	CLIP-seq
MIRT1176152	hsa-miR-3158-5p	CLIP-seq
MIRT1176153	hsa-miR-3175	CLIP-seq
MIRT1176154	hsa-miR-3180	CLIP-seq
MIRT1176155	hsa-miR-3180-3p	CLIP-seq
MIRT1176156	hsa-miR-3184	CLIP-seq
MIRT1176157	hsa-miR-3194-5p	CLIP-seq
MIRT1176158	hsa-miR-3196	CLIP-seq
MIRT1176159	hsa-miR-320a	CLIP-seq
MIRT1176160	hsa-miR-320b	CLIP-seq
MIRT1176161	hsa-miR-320c	CLIP-seq
MIRT1176162	hsa-miR-320d	CLIP-seq
MIRT1176163	hsa-miR-320e	CLIP-seq
MIRT1176164	hsa-miR-335	CLIP-seq
MIRT1176165	hsa-miR-342-5p	CLIP-seq
MIRT1176166	hsa-miR-34a	CLIP-seq
MIRT1176167	hsa-miR-34b	CLIP-seq
MIRT1176168	hsa-miR-34c-5p	CLIP-seq
MIRT1176169	hsa-miR-3612	CLIP-seq
MIRT1176170	hsa-miR-3659	CLIP-seq
MIRT1176171	hsa-miR-3661	CLIP-seq
MIRT1176172	hsa-miR-3678-3p	CLIP-seq
MIRT1176173	hsa-miR-370	CLIP-seq
MIRT1176174	hsa-miR-3972	CLIP-seq
MIRT1176175	hsa-miR-423-5p	CLIP-seq
MIRT1176176	hsa-miR-4260	CLIP-seq
MIRT1176177	hsa-miR-4261	CLIP-seq
MIRT1176178	hsa-miR-4268	CLIP-seq
MIRT1176179	hsa-miR-4270	CLIP-seq
MIRT1176180	hsa-miR-4271	CLIP-seq
MIRT1176181	hsa-miR-4290	CLIP-seq
MIRT1176182	hsa-miR-4314	CLIP-seq
MIRT1176183	hsa-miR-4320	CLIP-seq
MIRT1176184	hsa-miR-4429	CLIP-seq
MIRT1176185	hsa-miR-4441	CLIP-seq
MIRT1176186	hsa-miR-4448	CLIP-seq
MIRT1176187	hsa-miR-4461	CLIP-seq
MIRT1176188	hsa-miR-4488	CLIP-seq
MIRT1176189	hsa-miR-4492	CLIP-seq
MIRT1176190	hsa-miR-4498	CLIP-seq
MIRT1176191	hsa-miR-449a	CLIP-seq
MIRT1176192	hsa-miR-449b	CLIP-seq
MIRT1176193	hsa-miR-449c	CLIP-seq
MIRT1176194	hsa-miR-4535	CLIP-seq
MIRT1176195	hsa-miR-4640-5p	CLIP-seq
MIRT1176196	hsa-miR-4649-3p	CLIP-seq
MIRT1176197	hsa-miR-4651	CLIP-seq
MIRT1176198	hsa-miR-4656	CLIP-seq
MIRT1176199	hsa-miR-4658	CLIP-seq
MIRT1176200	hsa-miR-4664-5p	CLIP-seq
MIRT1176201	hsa-miR-4665-5p	CLIP-seq
MIRT1176202	hsa-miR-4667-5p	CLIP-seq
MIRT1176203	hsa-miR-4675	CLIP-seq
MIRT1176204	hsa-miR-4690-5p	CLIP-seq
MIRT1176205	hsa-miR-4695-5p	CLIP-seq
MIRT1176206	hsa-miR-4697-5p	CLIP-seq
MIRT1176207	hsa-miR-4700-5p	CLIP-seq
MIRT1176208	hsa-miR-4717-3p	CLIP-seq
MIRT1176209	hsa-miR-4722-3p	CLIP-seq
MIRT1176210	hsa-miR-4725-3p	CLIP-seq
MIRT1176211	hsa-miR-4726-5p	CLIP-seq
MIRT1176212	hsa-miR-4729	CLIP-seq
MIRT1176213	hsa-miR-4731-5p	CLIP-seq
MIRT1176214	hsa-miR-4741	CLIP-seq
MIRT1176215	hsa-miR-4743	CLIP-seq
MIRT1176216	hsa-miR-4758-5p	CLIP-seq
MIRT1176217	hsa-miR-4763-3p	CLIP-seq
MIRT1176218	hsa-miR-4800-5p	CLIP-seq
MIRT1176219	hsa-miR-492	CLIP-seq
MIRT1176220	hsa-miR-494	CLIP-seq
MIRT1176221	hsa-miR-548m	CLIP-seq
MIRT1176222	hsa-miR-593	CLIP-seq
MIRT1176223	hsa-miR-608	CLIP-seq
MIRT1176224	hsa-miR-609	CLIP-seq
MIRT1176225	hsa-miR-622	CLIP-seq
MIRT1176226	hsa-miR-631	CLIP-seq
MIRT1176227	hsa-miR-637	CLIP-seq
MIRT1176228	hsa-miR-644	CLIP-seq
MIRT1176229	hsa-miR-650	CLIP-seq
MIRT1176230	hsa-miR-762	CLIP-seq
MIRT1176231	hsa-miR-767-3p	CLIP-seq
MIRT1176232	hsa-miR-939	CLIP-seq
MIRT1176134	hsa-miR-1275	CLIP-seq
MIRT1176137	hsa-miR-147	CLIP-seq
MIRT1176164	hsa-miR-335	CLIP-seq
MIRT1176233	hsa-miR-4525	CLIP-seq
MIRT1176201	hsa-miR-4665-5p	CLIP-seq
MIRT1176234	hsa-miR-4723-5p	CLIP-seq
MIRT1176235	hsa-miR-521	CLIP-seq
MIRT1176236	hsa-miR-625	CLIP-seq
MIRT1176227	hsa-miR-637	CLIP-seq
MIRT1176228	hsa-miR-644	CLIP-seq
MIRT1176180	hsa-miR-4271	CLIP-seq
MIRT1176202	hsa-miR-4667-5p	CLIP-seq
MIRT1176207	hsa-miR-4700-5p	CLIP-seq
MIRT1176210	hsa-miR-4725-3p	CLIP-seq
MIRT2051034	hsa-miR-1234	CLIP-seq
MIRT1176135	hsa-miR-1287	CLIP-seq
MIRT1176137	hsa-miR-147	CLIP-seq
MIRT2051035	hsa-miR-1908	CLIP-seq
MIRT1176146	hsa-miR-2114	CLIP-seq
MIRT1176150	hsa-miR-3135b	CLIP-seq
MIRT1176151	hsa-miR-3150a-3p	CLIP-seq
MIRT1176153	hsa-miR-3175	CLIP-seq
MIRT1176164	hsa-miR-335	CLIP-seq
MIRT2051036	hsa-miR-3545-3p	CLIP-seq
MIRT1176169	hsa-miR-3612	CLIP-seq
MIRT1176173	hsa-miR-370	CLIP-seq
MIRT2051037	hsa-miR-4269	CLIP-seq
MIRT2051038	hsa-miR-4308	CLIP-seq
MIRT1176188	hsa-miR-4488	CLIP-seq
MIRT2051039	hsa-miR-4645-5p	CLIP-seq
MIRT1176202	hsa-miR-4667-5p	CLIP-seq
MIRT2051040	hsa-miR-4673	CLIP-seq
MIRT1176206	hsa-miR-4697-5p	CLIP-seq
MIRT1176207	hsa-miR-4700-5p	CLIP-seq
MIRT2051041	hsa-miR-4706	CLIP-seq
MIRT2051042	hsa-miR-4707-5p	CLIP-seq
MIRT2051043	hsa-miR-4728-5p	CLIP-seq
MIRT2051044	hsa-miR-4749-5p	CLIP-seq
MIRT2051045	hsa-miR-4755-3p	CLIP-seq
MIRT1176227	hsa-miR-637	CLIP-seq
MIRT1176228	hsa-miR-644	CLIP-seq
MIRT1176229	hsa-miR-650	CLIP-seq
MIRT2051046	hsa-miR-663	CLIP-seq
MIRT1176232	hsa-miR-939	CLIP-seq
MIRT1176140	hsa-miR-1909	CLIP-seq
MIRT1176180	hsa-miR-4271	CLIP-seq
MIRT1176202	hsa-miR-4667-5p	CLIP-seq
MIRT1176207	hsa-miR-4700-5p	CLIP-seq
MIRT1176210	hsa-miR-4725-3p	CLIP-seq
MIRT2280126	hsa-miR-127-5p	CLIP-seq
MIRT2280127	hsa-miR-4420	CLIP-seq
MIRT2280128	hsa-miR-4476	CLIP-seq
MIRT2280129	hsa-miR-4511	CLIP-seq
MIRT2280130	hsa-miR-4716-3p	CLIP-seq
MIRT2280131	hsa-miR-4733-3p	CLIP-seq

Show/Hide all (31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	21044950, 25416956, 32296183
GO:0005634	Component	Nucleus	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	IDA	23687301
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	ISS
GO:0010008	Component	Endosome membrane	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IDA	23687301
GO:0016020	Component	Membrane	IEA
GO:0030424	Component	Axon	ISS
GO:0030425	Component	Dendrite	IBA
GO:0030425	Component	Dendrite	IEA
GO:0030425	Component	Dendrite	ISS
GO:0031175	Process	Neuron projection development	IBA
GO:0031175	Process	Neuron projection development	IEA
GO:0031175	Process	Neuron projection development	ISS
GO:0042995	Component	Cell projection	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0043025	Component	Neuronal cell body	ISS
GO:0043204	Component	Perikaryon	IEA
GO:0045202	Component	Synapse	IEA
GO:0045453	Process	Bone resorption	IEA
GO:0048168	Process	Regulation of neuronal synaptic plasticity	IBA
GO:0048168	Process	Regulation of neuronal synaptic plasticity	IEA
GO:0098794	Component	Postsynapse	IEA
GO:0098794	Component	Postsynapse	IEA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0099149	Process	Regulation of postsynaptic neurotransmitter receptor internalization	IEA

MIM	HGNC	e!Ensembl
608458	17597	ENSG00000020129

Q9UBB6

Protein name

Neurochondrin

Protein 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 regu

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05536	Neurochondrin	30 → 637	Neurochondrin	Family

Tissue specificity

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. {ECO:0000269|PubMed:10524216, ECO:0000269|PubMed:9628581

Sequence

MSCCDLAAAGQLGKASIMASDCEPALNQAEGRNPTLERYLGALREAKNDSEQFAALLLVT
KAVKAGDIDAKTRRRIFDAVGFTFPNRLLTTKEAPDGCPDHVLRALGVALLACFCSDPEL
AAHPQVLNKIPILSTFLTARGDPDDAARRSMIDDTYQCLTAVAGTPRGPRHLIAGGTVSA
LCQAYLGHGYGFDQALALLVGLLAAAETQCWKEAEPDLLAVLRGLSEDFQKAEDASKFEL
CQLLPLFLPPTTVPPECYRDLQAGLARILGSKLSSWQRNPALKLAARLAHACGSDWIPAG
SSGSKFLALLVNLACVEVRLALEETGTEVKEDVVTACYALMELGIQECTRCEQSLLKEPQ
KVQLVSVMKEAIGAVIHYLLQVGSEKQKEPFVFASVRILGAWLAEETSSLRKEVCQLLPF
LVRYAKTLYEEAEEANDLSQQVANLAISPTTPGPTWPGDALRLLLPGWCHLTVEDGPREI
LIKEGAPSLLCKYFLQQWELTSPGHDTSVLPDSVEIGLQTCCHIFLNLVVTAPGLIKRDA
CFTSLMNTLMTSLPALVQQQGRLLLAANVATLGLLMARLLSTSPALQGTPASRGFFAAAI
LFLSQSHVARATPGSDQAVLALSPEYEGIWADLQELWFLGMQAFTGCVPLLPWLAPAALR
SRWPQELLQLLGSVSPNSVKPEMVAAYQGVLVELARANRLCREAMRLQAGEETASHYRMA
ALEQCLSEP

Sequence length

729

Interactions

View interactions

	KEGG
	Glutamatergic synapse

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Neurodevelopmental disorder with infantile epileptic spasms	Likely pathogenic; Pathogenic	rs2148538021, rs2148537359, rs376408289, rs1305972382, rs2148539394, rs762580458	RCV001775364 RCV002246199 RCV004801936 RCV004801937 RCV001526830 RCV001526831 View all (1 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AUTOSOMAL RECESSIVE NON-SYNDROMIC INTELLECTUAL DISABILITY	—	Disgenet, Orphanet Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NCDN-related disorder	Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (18)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Autoimmune Diseases	Autoimmune disease	Pubtator	39376559	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	29901136		★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	BEFREE	31138003		★★★★★ ★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	34875133	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypersensitivity Delayed	Hypersensitivity	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	25893345		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intervertebral disc disorder	Intervertebral Disc Disorder	BEFREE	29901136		★★★★★ ★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Learning Disabilities	Learning disorders	Pubtator	33711248	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Muscular Atrophy Spinal	Spinal muscular atrophy	Pubtator	29507115	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	33711248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinal Muscular Atrophy	Spinal Muscular Atrophy	BEFREE	29507115		★★★★★ ★☆☆☆☆ Found in Text Mining only

NCDN (neurochondrin)