NDN (necdin, MAGE family member)

Gene

• Entrez ID: 4692
• Gene name: Necdin, MAGE family member
• Gene symbol: NDN
• Synonyms: 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	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001764	Process	Neuron migration	IEA
GO:0003016	Process	Respiratory system process	IEA
GO:0005515	Function	Protein binding	IPI	21364888, 24722188, 32814053
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005813	Component	Centrosome	IEA
GO:0005829	Component	Cytosol	IDA
GO:0007413	Process	Axonal fasciculation	IEA
GO:0007417	Process	Central nervous system development	IEA
GO:0008285	Process	Negative regulation of cell population proliferation	IEA
GO:0008347	Process	Glial cell migration	IEA
GO:0009791	Process	Post-embryonic development	IEA
GO:0019221	Process	Cytokine-mediated signaling pathway	TAS
GO:0019233	Process	Sensory perception of pain	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0040008	Process	Regulation of growth	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043015	Function	Gamma-tubulin binding	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0043433	Process	Negative regulation of DNA-binding transcription factor activity	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0048011	Process	Neurotrophin TRK receptor signaling pathway	IEA
GO:0048675	Process	Axon extension	IEA
GO:0048871	Process	Multicellular organismal homeostasis	IEA
GO:0071514	Process	Genetic imprinting	IEA
GO:0090312	Process	Positive regulation of protein deacetylation	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

• Sequence:

  MSEQSKDLSDPNFAAEAPNSEVHSSPGVSEGVPPSATLAEPQSPPLGPTAAPQAAPPPQA
  PNDEGDPKALQQAAEEGRAHQAPSAAQPGPAPPAPAQLVQKAHELMWYVLVKDQKKMIIW
  FPDMVKDVIGSYKKWCRSILRRTSLILARVFGLHLRLTSLHTMEFALVKALEPEELDRVA
  LSNRMPMTGLLLMILSLIYVKGRGARESAVWNVLRILGLRPWKKHSTFGDVRKLITEEFV
  QMNYLKYQRVPYVEPPEYEFFWGSRASREITKMQIMEFLARVFKKDPQAWPSRYREALEE
  ARALREANPTAHYPRSSVSED

• Sequence length: 321

Pathways

Reactome:

Interleukin-4 and Interleukin-13 signaling

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Acromicric dysplasia	Acromicric Dysplasia	rs387906622, rs387906623, rs387906624, rs1131692052, rs387906626, rs587776863, rs1064797059, rs363806, rs1060501041, rs1555400049
Attention deficit hyperactivity disorder	Attention deficit hyperactivity disorder	rs120074176, rs786205019
Carcinoma	Carcinoma, Carcinoma, Spindle-Cell, Undifferentiated carcinoma	rs121912654, rs555607708, rs786202962, rs1564055259	21489049
Cryptorchidism	Cryptorchidism	rs121912555, rs104894697, rs104894698, rs398122886
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291, rs886041382, rs1057518991, rs1057518699, rs753254213, rs748294403, rs762552974, rs1135401795, rs1553121073, rs1553122926, rs1364690005, rs1554086554, rs1554210415, rs1554168326, rs1554776342, rs1553873247, rs1567860112, rs779009256, rs1557447255, rs1564568350, rs780011005, rs1597464953, rs1200336864, rs1569513017, rs1587459606, rs1570332505, rs748888652, rs1575155995, rs2087029320, rs1589669105, rs1601769604, rs1184981709, rs749201074
Hyperinsulinism	Hyperinsulinism	rs387906407, rs151344623, rs121913156, rs137853245, rs80356655, rs104894010, rs104894012, rs104894014, rs104894015, rs137852676, rs587783169, rs72559716, rs541269678, rs151344624, rs797045209, rs761749884, rs797045624, rs863225280, rs139964066, rs1057516281, rs1057516317, rs576684889, rs201682634, rs1350717554, rs768951263, rs1260178539, rs200670692, rs72559734, rs1400535021, rs372307320, rs1554923999, rs751279984, rs1008906426, rs367850779, rs1382448285, rs1564977373, rs750586210, rs1599937180
Hypogonadotropic hypogonadism	Hypogonadotropic hypogonadism	rs104894702, rs104893836, rs104893837, rs104893842, rs121909628, rs138249161, rs1601946139
Isolated somatotropin deficiency	Isolated somatotropin deficiency	rs797044450, rs71640277, rs863223306, rs2144738731, rs863223307, rs2144739370, rs863223309, rs863223310, rs137853223, rs2144739380, rs2144739391
Hypotonia	Neonatal Hypotonia	rs141138948, rs397517172, rs869312824, rs1583169151
Scoliosis	Scoliosis, unspecified	rs1057518828, rs147296805, rs758163506, rs1555613564, rs1596852902, rs1596853067, rs1596853085

Unknown
Disease name	Disease term	dbSNP ID	References
Acromicria	Acromicria
Anaplastic carcinoma	Anaplastic carcinoma		21489049
Clinodactyly	Clinodactyly of fingers, Clinodactyly
Dolichocephaly	Long narrow head
Dwarfism	Dwarfism
Hyperopia	Hyperopia
Motor delay	Clumsiness - motor delay
Penis agenesis	Penis agenesis
Physiologic amenorrhea	Primary physiologic amenorrhea
Prader-willi syndrome	Prader-Willi Syndrome, Prader-Willi syndrome due to paternal deletion of 15q11q13 type 1, Prader-Willi syndrome due to paternal deletion of 15q11q13 type 2, Prader-Willi syndrome due to imprinting mutation, Prader-Willi syndrome due to maternal uniparental disomy of chromosome 15	rs188762916, rs1555376130, rs35667483, rs74942536
Royer syndrome	Royer Syndrome
Sleep apnea	Sleep Apnea Syndromes
Somatotropin deficiency	Somatotropin deficiency
Specific learning disorder	Specific learning disability	rs1057519497