NUDC

nuclear distribution C, dynein complex regulator, the group of NudC family

Basic information

Region (hg38): 1:26900237-26946871

Links

ENSG00000090273 ∙ NCBI:10726 ∙ OMIM:610325 ∙ HGNC:8045 ∙ Uniprot:Q9Y266 ∙ 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 NUDC gene.

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.

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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in NUDC

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

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

Position	Type	Phenotype	Significance	ClinVar
1-26900238-T-C		not specified	Uncertain significance (May 27, 2022)
1-26900266-C-A		not specified	Uncertain significance (Mar 23, 2022)
1-26900337-A-G		not specified	Uncertain significance (May 30, 2024)
1-26900339-T-C		not specified	Uncertain significance (Jun 07, 2024)
1-26900364-C-A		not specified	Uncertain significance (Sep 12, 2023)
1-26900381-G-T		not specified	Uncertain significance (Apr 12, 2022)
1-26900418-C-G		not specified	Uncertain significance (Nov 08, 2022)
1-26900659-A-G		GPATCH3-related disorder	Likely benign (Aug 20, 2019)
1-26911850-T-C		NR0B2-related disorder	Uncertain significance (Aug 31, 2022)
1-26911864-TC-T			Uncertain significance (Apr 06, 2022)
1-26911868-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-26911870-A-G		Inherited obesity • NR0B2-related disorder	Uncertain significance (Dec 20, 2023)
1-26911880-C-T		NR0B2-related disorder	Uncertain significance (Nov 11, 2022)
1-26911885-T-C		NR0B2-related disorder • not specified	Uncertain significance (Jan 17, 2024)
1-26911901-T-C		NR0B2-related disorder	Uncertain significance (Jul 21, 2023)
1-26911907-G-A		Obesity • NR0B2-related disorder • not specified	Uncertain significance (Jan 30, 2024)
1-26911947-G-A			Likely benign (May 23, 2023)
1-26911960-G-A			Benign (Apr 22, 2023)
1-26911972-C-T		NR0B2-related disorder	Uncertain significance (Dec 18, 2023)
1-26911981-C-T		NR0B2-related disorder	Uncertain significance (Oct 20, 2023)
1-26911982-G-A		Inherited obesity	Uncertain significance (May 17, 2022)
1-26911987-T-C		NR0B2-related disorder	Uncertain significance (Feb 23, 2024)
1-26911994-C-T		NR0B2-related disorder	Uncertain significance (Dec 11, 2022)
1-26912001-C-T		NR0B2-related disorder	Uncertain significance (Oct 21, 2023)
1-26912036-C-A		Obesity, mild, early-onset • not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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