NDN

necdin, MAGE family member, the group of MAGE family

Basic information

Region (hg38): 15:23685399-23687305

Links

ENSG00000182636 ∙ NCBI:4692 ∙ OMIM:602117 ∙ HGNC:7675 ∙ Uniprot:Q99608 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDN gene.

• Inborn genetic diseases (14 variants)
• not provided (13 variants)
• Prader-Willi syndrome (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDN gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense			19	3	1	23
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	7	4

Variants in NDN

This is a list of pathogenic ClinVar variants found in the NDN region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-23686265-A-G			Benign/Likely benign (Dec 31, 2019)
15-23686269-T-C			Likely benign (Dec 31, 2019)
15-23686316-G-A		not specified	Uncertain significance (Jan 09, 2024)
15-23686346-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-23686347-G-T		Prader-Willi syndrome	Uncertain significance (Oct 21, 2021)
15-23686353-C-T			Uncertain significance (Mar 01, 2022)
15-23686360-G-A			Benign (May 02, 2023)
15-23686380-C-A		not specified	Uncertain significance (Aug 12, 2021)
15-23686422-C-T		not specified	Uncertain significance (Feb 14, 2023)
15-23686450-G-A			Benign (Dec 31, 2019)
15-23686489-A-T		not specified	Uncertain significance (Jun 29, 2022)
15-23686495-T-C		NDN-related disorder	Likely benign (Mar 18, 2019)
15-23686528-G-A			Likely benign (Jul 17, 2018)
15-23686569-G-A			Benign (Dec 31, 2019)
15-23686616-T-C			Uncertain significance (Dec 30, 2020)
15-23686659-T-C		not specified	Uncertain significance (Dec 15, 2023)
15-23686685-C-T		Prader-Willi syndrome	Uncertain significance (Mar 05, 2018)
15-23686714-G-A			Likely benign (Oct 01, 2022)
15-23686745-G-GT		Prader-Willi syndrome	Uncertain significance (Oct 17, 2018)
15-23686800-G-T		not specified	Uncertain significance (Jun 12, 2023)
15-23686805-C-T		not specified	Uncertain significance (Jun 29, 2022)
15-23686832-A-G		not specified	Uncertain significance (Jun 06, 2023)
15-23686878-G-C			Uncertain significance (Oct 29, 2019)
15-23686955-G-A			Benign (Dec 31, 2019)
15-23686974-C-A		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDN	protein_coding	protein_coding	ENST00000331837	1	1886

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.675	0.321	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.707	167	195	0.857	0.0000119	2053
Missense in Polyphen		64	94.544	0.67693		956
Synonymous	-1.06	104	91.1	1.14	0.00000631	660
Loss of Function	2.28	1	7.95	0.126	3.42e-7	84

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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 E1A, and the transcription factor E2F. Necdin also interacts with p53 and works in an additive manner to inhibit cell growth. Functions also as transcription factor and binds directly to specific guanosine-rich DNA sequences (By similarity). {ECO:0000250}.
• Pathway: Adipogenesis;Prader-Willi and Angelman Syndrome;Interleukin-4 and 13 signaling;p75(NTR)-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.205

Intolerance Scores

• loftool: 0.230
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.13

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.603
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ndn
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neuron migration;respiratory system process;nervous system development;axonal fasciculation;central nervous system development;negative regulation of cell population proliferation;glial cell migration;post-embryonic development;cytokine-mediated signaling pathway;sensory perception of pain;regulation of growth;positive regulation of transcription by RNA polymerase II;neurotrophin TRK receptor signaling pathway;axon extension;multicellular organismal homeostasis;genetic imprinting
• Cellular component: nucleoplasm;centrosome;cytosol;cell projection;perikaryon
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;gamma-tubulin binding