NDEL1
nudE neurodevelopment protein 1 like 1
Basic information
Region (hg38): 17:8413131-8490411
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NDEL1 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in NDEL1
This is a list of pathogenic ClinVar variants found in the NDEL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-8444291-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 17-8448557-A-G | not specified | Uncertain significance (Jul 08, 2022) | ||
| 17-8450824-A-G | not specified | Uncertain significance (Sep 17, 2021) | ||
| 17-8450948-C-T | not specified | Uncertain significance (May 26, 2023) | ||
| 17-8460084-A-T | not specified | Uncertain significance (Oct 06, 2021) | ||
| 17-8460112-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 17-8460130-G-A | not specified | Uncertain significance (Jun 16, 2023) | ||
| 17-8460156-A-C | not specified | Uncertain significance (Nov 07, 2022) | ||
| 17-8466970-C-A | not specified | Uncertain significance (May 23, 2023) | ||
| 17-8466980-C-T | not specified | Uncertain significance (Apr 30, 2024) | ||
| 17-8466982-C-T | not specified | Uncertain significance (Sep 12, 2023) | ||
| 17-8466989-C-T | not specified | Uncertain significance (Apr 04, 2024) | ||
| 17-8466998-C-T | not specified | Uncertain significance (Jan 02, 2024) | ||
| 17-8475843-G-A | MYH10-related disorder | Benign (Nov 15, 2018) | ||
| 17-8475850-C-G | Inborn genetic diseases | Uncertain significance (May 06, 2022) | ||
| 17-8475898-A-G | Inborn genetic diseases | Uncertain significance (Dec 01, 2022) | ||
| 17-8475904-C-T | Jaw-winking syndrome | Uncertain significance (Feb 26, 2024) | ||
| 17-8475908-G-A | Inborn genetic diseases | Uncertain significance (Oct 03, 2023) | ||
| 17-8475916-C-G | Inborn genetic diseases | Uncertain significance (Mar 31, 2023) | ||
| 17-8475920-TG-T | Uncertain significance (Apr 29, 2022) | |||
| 17-8475947-G-A | Inborn genetic diseases | Uncertain significance (Oct 27, 2023) | ||
| 17-8476883-G-A | Uncertain significance (Nov 09, 2017) | |||
| 17-8476897-C-G | Uncertain significance (Feb 16, 2023) | |||
| 17-8476906-C-T | Inborn genetic diseases | Uncertain significance (May 02, 2023) | ||
| 17-8476919-C-G | Inborn genetic diseases | Uncertain significance (May 24, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NDEL1 | protein_coding | protein_coding | ENST00000334527 | 8 | 77281 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.984 | 0.0165 | 125739 | 0 | 4 | 125743 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.66 | 124 | 188 | 0.660 | 0.0000102 | 2219 |
| Missense in Polyphen | 23 | 66.671 | 0.34498 | 805 | ||
| Synonymous | 0.838 | 68 | 77.4 | 0.879 | 0.00000461 | 679 |
| Loss of Function | 3.88 | 2 | 21.3 | 0.0939 | 0.00000125 | 248 |
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 | 0.0000463 | 0.0000462 |
| 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: Required for organization of the cellular microtubule array and microtubule anchoring at the centrosome. May regulate microtubule organization at least in part by targeting the microtubule severing protein KATNA1 to the centrosome. Also positively regulates the activity of the minus-end directed microtubule motor protein dynein. May enhance dynein-mediated microtubule sliding by targeting dynein to the microtubule plus ends. Required for several dynein- and microtubule-dependent processes such as the maintenance of Golgi integrity, the centripetal motion of secretory vesicles and the coupling of the nucleus and centrosome. Also required during brain development for the migration of newly formed neurons from the ventricular/subventricular zone toward the cortical plate. Plays a role, together with DISC1, in the regulation of neurite outgrowth. Required for mitosis in some cell types but appears to be dispensible for mitosis in cortical neuronal progenitors, which instead requires NDE1. Facilitates the polymerization of neurofilaments from the individual subunits NEFH and NEFL. Positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts (By similarity). {ECO:0000250|UniProtKB:Q9ERR1, ECO:0000269|PubMed:12556484, ECO:0000269|PubMed:14970193, ECO:0000269|PubMed:16291865, ECO:0000269|PubMed:17600710}.;
- Pathway
- Signal Transduction;lissencephaly gene (lis1) in neuronal migration and development;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;Aurora A signaling;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Lissencephaly gene (LIS1) in neuronal migration and development
(Consensus)
Recessive Scores
- pRec
- 0.179
Intolerance Scores
- loftool
- 0.0826
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.53
Haploinsufficiency Scores
- pHI
- 0.666
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.449
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.820
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ndel1
- 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); 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); embryo phenotype; cellular phenotype;
Gene ontology
- Biological process
- establishment of mitotic spindle orientation;neuron migration;inner cell mass cell proliferation;proteolysis;microtubule nucleation;chromosome segregation;mitotic centrosome separation;retrograde axonal transport;insulin receptor signaling pathway;regulation of neuron projection development;cell migration;cerebral cortex radially oriented cell migration;central nervous system neuron axonogenesis;lysosome localization;regulation of intracellular protein transport;positive regulation of GTPase activity;positive regulation of axon extension;vesicle transport along microtubule;positive regulation of axon regeneration;nuclear envelope disassembly;establishment of chromosome localization;centrosome localization;neurofilament cytoskeleton organization;activation of GTPase activity;positive regulation of ruffle assembly;neuron projection extension;regulation of microtubule motor activity
- Cellular component
- kinetochore;condensed chromosome kinetochore;nuclear envelope;centrosome;spindle;cytosol;kinesin complex;microtubule;synaptic vesicle;cell leading edge;axon hillock;neurofilament cytoskeleton;central region of growth cone;axon cytoplasm
- Molecular function
- protein binding;microtubule binding;identical protein binding;alpha-tubulin binding;protein-containing complex binding;beta-tubulin binding;oligopeptidase activity