NUDC
Basic information
Region (hg38): 1:26900238-26946871
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (49 variants)
- NUDC-related_condition (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006600.4. 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 | 1 | |||||
| missense | 49 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDC | protein_coding | protein_coding | ENST00000321265 | 9 | 46625 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.887 | 0.113 | 125740 | 0 | 7 | 125747 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.794 | 157 | 188 | 0.837 | 0.0000122 | 2203 |
| Missense in Polyphen | 31 | 54.938 | 0.56427 | 698 | ||
| Synonymous | -0.0291 | 71 | 70.7 | 1.00 | 0.00000429 | 591 |
| Loss of Function | 3.56 | 3 | 20.3 | 0.148 | 0.00000115 | 227 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000151 | 0.000148 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in neurogenesis and neuronal migration (By similarity). Necessary for correct formation of mitotic spindles and chromosome separation during mitosis. Necessary for cytokinesis and cell proliferation. {ECO:0000250, ECO:0000269|PubMed:12679384, ECO:0000269|PubMed:12852857}.;
- Pathway
- Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Mitotic Telophase/Cytokinesis;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;PLK1 signaling events;Lissencephaly gene (LIS1) in neuronal migration and development
(Consensus)
Recessive Scores
- pRec
- 0.0913
Intolerance Scores
- loftool
- 0.277
- rvis_EVS
- -0.52
- rvis_percentile_EVS
- 21.2
Haploinsufficiency Scores
- pHI
- 0.350
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.597
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nudc
- Phenotype
Zebrafish Information Network
- Gene name
- nudc
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- curved
Gene ontology
- Biological process
- protein folding;cell cycle;multicellular organism development;cell population proliferation;developmental process;cell division
- Cellular component
- nucleoplasm;cytoplasm;cytosol;microtubule
- Molecular function
- protein binding;cadherin binding;unfolded protein binding