NDEL1

nudE neurodevelopment protein 1 like 1

Basic information

Region (hg38): 17:8413130-8490411

Links

ENSG00000166579 ∙ NCBI:81565 ∙ OMIM:607538 ∙ HGNC:17620 ∙ Uniprot:Q9GZM8 ∙ 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 NDEL1 gene.

• Inborn genetic diseases (8 variants)

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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	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
17-8448557-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)
17-8466982-C-T		not specified	Uncertain significance (Sep 12, 2023)
17-8466998-C-T		not specified	Uncertain significance (Jan 02, 2024)
17-8475843-G-A		MYH10-related disorder	Benign/Likely benign (Feb 18, 2019)
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)
17-8476920-G-A		MYH10-related disorder	Likely benign (May 08, 2019)
17-8476949-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
17-8476978-C-T			Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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