NDN
necdin, MAGE family member, the group of MAGE family
Basic information
Region (hg38): 15:23685400-23687305
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
- not_provided (15 variants)
- Prader-Willi_syndrome (4 variants)
- NDN-related_disorder (2 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. These statistics are base on transcript: NM_000002487.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 10 | |||||
| missense | 43 | 47 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 44 | 10 | 4 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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