NUF2

NUF2 component of NDC80 kinetochore complex, the group of NDC80 kinetochore complex

Basic information

Region (hg38): 1:163266576-163355764

Previous symbols: [ "CDCA1" ]

Links

ENSG00000143228NCBI:83540OMIM:611772HGNC:14621Uniprot:Q9BZD4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUF2 gene.

  • not provided (1 variants)
  • Short stature;Microcephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUF2 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
1
clinvar
21
clinvar
1
clinvar
23
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 1 0 21 1 0

Variants in NUF2

This is a list of pathogenic ClinVar variants found in the NUF2 region.

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

Position Type Phenotype Significance ClinVar
1-163326071-C-G not specified Uncertain significance (Jun 02, 2023)2555977
1-163326094-G-T not specified Uncertain significance (May 01, 2024)3301419
1-163326142-C-G not specified Uncertain significance (Nov 21, 2022)2328898
1-163328253-A-G not specified Uncertain significance (Jun 11, 2024)2294027
1-163328868-C-T not specified Uncertain significance (Oct 25, 2023)3202844
1-163328869-G-A not specified Uncertain significance (Aug 08, 2022)2305995
1-163336760-G-C not specified Uncertain significance (Dec 15, 2022)2335738
1-163336784-T-G Short stature;Microcephaly Pathogenic (Dec 22, 2020)992629
1-163336816-C-T not specified Uncertain significance (Oct 13, 2021)2391728
1-163336817-G-A not specified Uncertain significance (Feb 28, 2024)3202845
1-163336836-T-G not specified Uncertain significance (Sep 29, 2022)2314679
1-163338030-C-T not specified Likely benign (Dec 13, 2023)3202846
1-163338034-C-A not specified Uncertain significance (Aug 13, 2021)2244390
1-163339467-A-C not specified Uncertain significance (Apr 07, 2022)2222502
1-163343845-C-T not specified Uncertain significance (Oct 26, 2021)2218094
1-163345778-T-C 4p partial monosomy syndrome Uncertain significance (-)1684154
1-163347765-C-G not specified Uncertain significance (Jan 23, 2024)3202847
1-163347798-G-C not specified Uncertain significance (Nov 13, 2023)3202848
1-163347853-G-A not specified Uncertain significance (Apr 07, 2023)2534131
1-163348963-A-C not specified Uncertain significance (Mar 23, 2022)2279702
1-163348974-G-T not specified Uncertain significance (Aug 14, 2023)2618281
1-163355367-G-C not specified Uncertain significance (Nov 01, 2022)2321942
1-163355383-A-G not specified Uncertain significance (Feb 17, 2024)3202843
1-163355398-G-A not specified Uncertain significance (Apr 25, 2023)2518093
1-163355453-T-G not specified Uncertain significance (May 01, 2024)3301418

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NUF2protein_codingprotein_codingENST00000271452 1389189
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003820.9981256250941257190.000374
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.371732320.7470.00001183073
Missense in Polyphen4057.5350.69523781
Synonymous0.8657180.90.8780.00000434776
Loss of Function2.711227.30.4400.00000131372

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001200.000120
Ashkenazi Jewish0.000.00
East Asian0.0003810.000381
Finnish0.001120.00111
European (Non-Finnish)0.0005030.000501
Middle Eastern0.0003810.000381
South Asian0.00003270.0000327
Other0.0003290.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a component of the essential kinetochore- associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity (PubMed:12438418, PubMed:14654001, PubMed:15062103, PubMed:15235793, PubMed:15239953, PubMed:15548592, PubMed:17535814). Required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore (PubMed:15548592). The NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerizing microtubules (PubMed:23085020). {ECO:0000269|PubMed:12438418, ECO:0000269|PubMed:14654001, ECO:0000269|PubMed:15062103, ECO:0000269|PubMed:15235793, ECO:0000269|PubMed:15239953, ECO:0000269|PubMed:15548592, ECO:0000269|PubMed:17535814, ECO:0000269|PubMed:23085020}.;
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;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec
0.124

Intolerance Scores

loftool
0.907
rvis_EVS
-0.07
rvis_percentile_EVS
48.69

Haploinsufficiency Scores

pHI
0.282
hipred
Y
hipred_score
0.717
ghis
0.666

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.906

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Nuf2
Phenotype

Zebrafish Information Network

Gene name
nuf2
Affected structure
head
Phenotype tag
abnormal
Phenotype quality
flat

Gene ontology

Biological process
mitotic spindle organization;chromosome segregation;meiotic chromosome segregation;cell division;attachment of mitotic spindle microtubules to kinetochore;kinetochore organization
Cellular component
chromosome, centromeric region;condensed nuclear chromosome kinetochore;nucleus;cytosol;membrane;Ndc80 complex
Molecular function
molecular_function;protein binding;protein-containing complex binding