NDN (necdin, MAGE family member)

Gene

• Entrez ID: 4692
• Gene name: Necdin, MAGE family member
• Gene symbol: NDN
• Synonyms (NCBI Gene): HsT16328, PWCR
• Chromosome: 15
• Chromosome location: 15q11.2
• Summary: This intronless gene is located in the Prader-Willi syndrome deletion region. It is an imprinted gene and is expressed exclusively from the paternal allele. Studies in mouse suggest that the protein encoded by this gene may suppress growth in postmitotic

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019333	hsa-miR-148b-3p	Microarray	17612493
MIRT2280570	hsa-miR-4798-3p	CLIP-seq
MIRT2280571	hsa-miR-561	CLIP-seq
MIRT2438958	hsa-miR-145	CLIP-seq
MIRT2438959	hsa-miR-3591-5p	CLIP-seq
MIRT2438960	hsa-miR-3671	CLIP-seq
MIRT2438961	hsa-miR-4280	CLIP-seq
MIRT2438962	hsa-miR-455-3p	CLIP-seq
MIRT2438963	hsa-miR-4786-5p	CLIP-seq
MIRT2438964	hsa-miR-607	CLIP-seq
MIRT2438965	hsa-miR-769-5p	CLIP-seq
MIRT2579054	hsa-miR-1295	CLIP-seq
MIRT2438958	hsa-miR-145	CLIP-seq
MIRT2579055	hsa-miR-3145-5p	CLIP-seq
MIRT2579056	hsa-miR-3179	CLIP-seq
MIRT2438959	hsa-miR-3591-5p	CLIP-seq
MIRT2438960	hsa-miR-3671	CLIP-seq
MIRT2579057	hsa-miR-3692	CLIP-seq
MIRT2579058	hsa-miR-3974	CLIP-seq
MIRT2438961	hsa-miR-4280	CLIP-seq
MIRT2579059	hsa-miR-4299	CLIP-seq
MIRT2579060	hsa-miR-4512	CLIP-seq
MIRT2438962	hsa-miR-455-3p	CLIP-seq
MIRT2579061	hsa-miR-4652-3p	CLIP-seq
MIRT2579062	hsa-miR-4710	CLIP-seq
MIRT2438963	hsa-miR-4786-5p	CLIP-seq
MIRT2579063	hsa-miR-4792	CLIP-seq
MIRT2579064	hsa-miR-508-5p	CLIP-seq
MIRT2579065	hsa-miR-578	CLIP-seq
MIRT2438964	hsa-miR-607	CLIP-seq
MIRT2579066	hsa-miR-609	CLIP-seq
MIRT2438965	hsa-miR-769-5p	CLIP-seq
MIRT2579054	hsa-miR-1295	CLIP-seq
MIRT2686014	hsa-miR-138	CLIP-seq
MIRT2438958	hsa-miR-145	CLIP-seq
MIRT2579055	hsa-miR-3145-5p	CLIP-seq
MIRT2686015	hsa-miR-3164	CLIP-seq
MIRT2579056	hsa-miR-3179	CLIP-seq
MIRT2438959	hsa-miR-3591-5p	CLIP-seq
MIRT2438960	hsa-miR-3671	CLIP-seq
MIRT2579058	hsa-miR-3974	CLIP-seq
MIRT2438961	hsa-miR-4280	CLIP-seq
MIRT2579059	hsa-miR-4299	CLIP-seq
MIRT2579060	hsa-miR-4512	CLIP-seq
MIRT2438962	hsa-miR-455-3p	CLIP-seq
MIRT2579061	hsa-miR-4652-3p	CLIP-seq
MIRT2686016	hsa-miR-4778-3p	CLIP-seq
MIRT2438963	hsa-miR-4786-5p	CLIP-seq
MIRT2579064	hsa-miR-508-5p	CLIP-seq
MIRT2579065	hsa-miR-578	CLIP-seq
MIRT2438964	hsa-miR-607	CLIP-seq
MIRT2579066	hsa-miR-609	CLIP-seq
MIRT2686017	hsa-miR-617	CLIP-seq
MIRT2438965	hsa-miR-769-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0001764	Process	Neuron migration	IEA
GO:0003016	Process	Respiratory system process	IEA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	21364888, 24722188, 32529326, 32814053, 34591642
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0007409	Process	Axonogenesis	IEA
GO:0007413	Process	Axonal fasciculation	IEA
GO:0007417	Process	Central nervous system development	IEA
GO:0007585	Process	Respiratory gaseous exchange by respiratory system	IEA
GO:0008347	Process	Glial cell migration	IEA
GO:0009791	Process	Post-embryonic development	IEA
GO:0019233	Process	Sensory perception of pain	IEA
GO:0030182	Process	Neuron differentiation	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043015	Function	Gamma-tubulin binding	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048011	Process	Neurotrophin TRK receptor signaling pathway	IEA
GO:0048666	Process	Neuron development	IEA
GO:0048675	Process	Axon extension	IEA
GO:0048871	Process	Multicellular organismal-level homeostasis	IEA
GO:0071514	Process	Genomic imprinting	IEA
GO:1990841	Function	Promoter-specific chromatin binding	IEA

Other IDs

• MIM: 602117
• HGNC: 7675
• e!Ensembl: ENSG00000182636

Protein

• UniProt ID: Q99608
• Protein name: Necdin
• Protein function: Growth suppressor that facilitates the entry of the cell into cell cycle arrest. Functionally similar to the retinoblastoma protein it binds to and represses the activity of cell-cycle-promoting proteins such as SV40 large T antigen, adenovirus
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01454	MAGE	157 → 273	MAGE family	Family

• Tissue specificity: TISSUE SPECIFICITY: Almost ubiquitous. Detected in fetal brain, lung, liver and kidney; in adult heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine and colon. Not detected in pe
• Sequence:

  MSEQSKDLSDPNFAAEAPNSEVHSSPGVSEGVPPSATLAEPQSPPLGPTAAPQAAPPPQA
  PNDEGDPKALQQAAEEGRAHQAPSAAQPGPAPPAPAQLVQKAHELMWYVLVKDQKKMIIW
  FPDMVKDVIGSYKKWCRSILRRTSLILARVFGLHLRLTSLHTMEFALVKALEPEELDRVA
  LSNRMPMTGLLLMILSLIYVKGRGARESAVWNVLRILGLRPWKKHSTFGDVRKLITEEFV
  QMNYLKYQRVPYVEPPEYEFFWGSRASREITKMQIMEFLARVFKKDPQAWPSRYREALEE
  ARALREANPTAHYPRSSVSED

• Sequence length: 321

Pathways

Reactome:

Interleukin-4 and Interleukin-13 signaling

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CARCINOMA	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NDN-related disorder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OLIGODENDROGLIOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prader-Willi syndrome	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
PRADER-WILLI SYNDROME DUE TO IMPRINTING MUTATION	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRADER-WILLI SYNDROME DUE TO MATERNAL UNIPARENTAL DISOMY OF CHROMOSOME 15	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRADER-WILLI SYNDROME DUE TO PATERNAL DELETION OF 15Q11Q13 TYPE 1	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRADER-WILLI SYNDROME DUE TO PATERNAL DELETION OF 15Q11Q13 TYPE 2	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acromicria	Acromicria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Acromicric Dysplasia	Acromicric Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anaplastic carcinoma	Anaplastic Carcinoma	CTD_human_DG	21489049		★☆☆☆☆ Found in Text Mining only
Angelman Syndrome	Angelman Syndrome	BEFREE	8188222		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	11782285, 24239951		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	Pubtator	18835857	Associate	★☆☆☆☆ Found in Text Mining only
Bardet-Biedl Syndrome	Bardet-Biedl Syndrome	BEFREE	15649943		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	22046235, 26384308		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	22046235	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	CTD_human_DG	21489049		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	26689988		★☆☆☆☆ Found in Text Mining only
Carcinoma, Spindle-Cell	Carcinoma	CTD_human_DG	21489049		★☆☆☆☆ Found in Text Mining only
Clinodactyly	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	28521288		★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Development Disorder	BEFREE	20665884		★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	22245613		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	22245613		★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathy	Diabetic Nephropathy	BEFREE	22245613		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	BEFREE	10915770		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	32170852	Associate	★☆☆☆☆ Found in Text Mining only
Esophageal Squamous Cell Carcinoma	Esophageal squamous cell carcinoma	Pubtator	12901795	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	21525872		★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	Pubtator	21525872	Inhibit	★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	21525872		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	20665884, 29152105		★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Graves Disease	Graves Disease	BEFREE	10943736		★☆☆☆☆ Found in Text Mining only
HSAN Type IV	Hereditary insensitivity to pain with anhidrosis	BEFREE	25316729		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hyperopia	Hyperopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypogonadism, Isolated Hypogonadotropic	Hypogonadism	BEFREE	21543378		★☆☆☆☆ Found in Text Mining only
Hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	BEFREE	21543378		★☆☆☆☆ Found in Text Mining only
Hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Idiopathic hypogonadotropic hypogonadism	Hypogonadotropic Hypogonadism	BEFREE	21543378		★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	22138333	Associate	★☆☆☆☆ Found in Text Mining only
Isolated somatotropin deficiency	Isolated Somatotropin Deficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Kallmann Syndrome	Kallmann Syndrome	BEFREE	21543378		★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	22245613		★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	29152105		★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	22046235, 26384308		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	22355404, 26689988		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of testis	Malignant Neoplasm Of Testis	BEFREE	11901543		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	10891541, 22046235, 22355404, 23549060, 26689988		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	26384308		★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	21073635, 22046235		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	22046235	Inhibit	★☆☆☆☆ Found in Text Mining only
Mental disorders	Mental Disorders	BEFREE	20467835		★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19626646, 22355404, 23549060, 26689988		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	21150695, 26971449		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	Pubtator	39217334	Associate	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	25187168		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	BEFREE	20665884, 22305984, 28973533		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	21233802	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	27158277	Inhibit	★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	26689988		★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	22046235	Inhibit	★☆☆☆☆ Found in Text Mining only
Ovarian Neoplasms	Ovarian neoplasm	Pubtator	23549060	Associate	★☆☆☆☆ Found in Text Mining only
Paranoid Disorders	Paranoia	Pubtator	29343559	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	26971449		★☆☆☆☆ Found in Text Mining only
Penis agenesis	Penis Agenesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Prader-Willi Syndrome	Prader-Willi Syndrome	BEFREE	10713459, 10802660, 10915770, 11782285, 11891783, 15565282, 15634360, 15649943, 18272695, 18557765, 18930956, 19066619, 19421899, 19626646, 19712904, 20665884, 21150695, 21543378, 21912643, 22305984, 23314527, 24039599, 24704109, 28213671, 28973533, 29087295, 9302265, 9354807, 9412790, 9630521, 9691003		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Prader-Willi Syndrome	Prader-Willi Syndrome	CTD_human_DG			★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Prader-Willi syndrome due to imprinting mutation	Prader-Willi Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	Prader-Willi Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1	Prader-Willi Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2	Prader-Willi Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary physiologic amenorrhea	Physiologic Amenorrhea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	24513574	Associate	★☆☆☆☆ Found in Text Mining only
Rett Syndrome	Rett Syndrome	BEFREE	12107440		★☆☆☆☆ Found in Text Mining only
Royer Syndrome	Royer Syndrome	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	Pubtator	29343559	Associate	★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sleep Apnea Syndromes	Sleep Apnea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Somatotropin deficiency	Somatotropin Deficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	26518708		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	26518708	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of the head and neck	Carcinoma Of The Head And Neck	BEFREE	26518708		★☆☆☆☆ Found in Text Mining only
Systemic Scleroderma	Scleroderma	LHGDN	12913118		★☆☆☆☆ Found in Text Mining only
Undifferentiated carcinoma	Carcinoma	CTD_human_DG	21489049		★☆☆☆☆ Found in Text Mining only
Urothelial Carcinoma	Urothelial Carcinoma	BEFREE	18644980, 23549060		★☆☆☆☆ Found in Text Mining only