NUDC

protein-coding

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

Gene summary

This gene encodes a nuclear distribution protein that plays an essential role in mitosis and cytokinesis. The encoded protein is involved in spindle formation during mitosis and in microtubule organization during cytokinesis. Pseudogenes of this gene are found on chromosome 2. [provided by RefSeq, Feb 2012]

MANE transcript

NM_006600.4

Inheritance

—

ClinVar variants

U:55B:1

Top phenotype

NUDC-related condition

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr1:26,900,238-26,946,871

External References & Databases

Ensembl (ENSG00000090273)

Transcript & Mutation Effects

hg38 • Region Span ~46.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUDC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

NUDC-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006600.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			49 clinvar			49
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	55	1	0	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 78 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006600.4	RefSeq	NP_006591.1	9	MANE Select
ENST00000321265.10	Ensembl	ENSP00000319664.5	9	MANE Select
ENST00000435827.6	Ensembl	ENSP00000404020.2	5	Standard
ENST00000452707.1	Ensembl	ENSP00000400981.1	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nudc	Danio rerio	Structure: whole organism Quality: curved abnormal

Gene / Model

Organism

Observed Phenotype

nudc

Danio rerio

Structure: whole organism

Quality: curved

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

protein folding
cell cycle
multicellular organism development
cell population proliferation
developmental process

Molecular Function

protein binding
cadherin binding
unfolded protein binding

Cellular Component

nucleoplasm
cytoplasm
cytosol
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321265
Coding exons: 9
Length: 46625
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125747
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.794	157	188	0.837	0.0000122	2203
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0913

Intolerance Scores

LoFtool: 0.277
RVIS EVS: -0.52
RVIS percentile EVS: 21.2

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium