NDN necdin, MAGE family member [Homo sapiens (human)] - Gene

Summary

Official Symbol: NDNprovided by HGNC
Official Full Name: necdin, MAGE family memberprovided by HGNC
Primary source: HGNC:HGNC:7675
See related: Ensembl:ENSG00000182636 MIM:602117; AllianceGenome:HGNC:7675
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: PWCR; HsT16328
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 neurons. [provided by RefSeq, Jul 2008]
Orthologs: mouse all
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Genomic context

Location:: 15q11.2

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (23685400..23687305, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (21419888..21421793, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (23930547..23932452, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry.
Title: The necdin interactome: evaluating the effects of amino acid substitutions and cell stress using proximity-dependent biotinylation (BioID) and mass spectrometry.
We focused on three important regulatory DNA elements which are all differentially methylated regions (DMRs), methylated on the maternal allele: the PWS imprinting center (PWS-IC), which is a germline DMR and the somatic NDN and MKRN3 DMRs, hierarchically controlled by PWS-IC.
Title: Loss of hierarchical imprinting regulation at the Prader-Willi/Angelman syndrome locus in human iPSCs.
the single-nucleotide polymorphism rs850807, which is putatively functional and linked with MAGEL2 and NDN Genetic variation in rs850807 was strongly and exclusively associated with the ideas of reference subscale of the schizophrenia spectrum, which is best typified as paranoia
Title: A genetic locus for paranoia.
this study shows that hypermethylation of NDN promotes cell proliferation by activating the Wnt signaling pathway in colorectal cancer
Title: Hypermethylation of NDN promotes cell proliferation by activating the Wnt signaling pathway in colorectal cancer.
One candidate variant was located in an alpha helix of Necdin (NDN), phased to the paternally inherited allele. NDN is maternally imprinted within the 15q11.2 Prader-Willi Syndrome (PWS) region
Title: Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants.
NDN is an imprinted tumor suppressor gene which affects cancer cell motility, invasion and growth and that its loss of function in ovarian cancer can be caused by both genetic and epigenetic mechanisms.
Title: NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms.
Germline single nucleotide polymorphism in necdin gene is associated with breast cancer.
Title: Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc.
NDN and CD1A are novel prognostic methylation markers in patients with head and neck squamous carcinomas
Title: NDN and CD1A are novel prognostic methylation markers in patients with head and neck squamous carcinomas.
Necdin expression declined during replicative aging of IMR90 primary human fibroblasts or after induction of premature senescence.Showed that in normal human cells, Necdin expression mimicked the effect of p53 inactivation by increasing radioresistance.
Title: Necdin modulates proliferative cell survival of human cells in response to radiation-induced genotoxic stress.
Hypermethylation and mutation of necdin is associated with neoplasms.
Title: Putative tumour suppressor gene necdin is hypermethylated and mutated in human cancer.

Submit: New GeneRIF Correction See all GeneRIFs (27)

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

Copy number response

Description
Copy number response Haploinsufficency No evidence available (Last evaluated 2012-04-26) ClinGen Genome Curation Page Triplosensitivity No evidence available (Last evaluated 2012-04-26) ClinGen Genome Curation Page

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

NDN_940 (e-PCR)
- UniSTS:277526

PMC24540P1 (e-PCR)
- UniSTS:272262

SGC30582 (e-PCR)
- UniSTS:76240

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables gamma-tubulin binding	IEA Inferred from Electronic Annotation more info
enables promoter-specific chromatin binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axon extension	IEA Inferred from Electronic Annotation more info
involved_in axonal fasciculation	IEA Inferred from Electronic Annotation more info
involved_in central nervous system development	IEA Inferred from Electronic Annotation more info
involved_in genomic imprinting	IEA Inferred from Electronic Annotation more info
involved_in glial cell migration	IEA Inferred from Electronic Annotation more info
involved_in multicellular organismal-level homeostasis	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron migration	IEA Inferred from Electronic Annotation more info
involved_in neurotrophin TRK receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein deacetylation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
involved_in respiratory system process	IEA Inferred from Electronic Annotation more info
involved_in sensory perception of pain	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in perikaryon	IEA Inferred from Electronic Annotation more info
part_of protein-containing complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: necdin

Names: Prader-Willi syndrome chromosome region; necdin homolog; necdin, melanoma antigen (MAGE) family member; necdin-like protein

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.