NUF2

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

Basic information

Region (hg38): 1:163266575-163355764

Previous symbols: [ "CDCA1" ]

Links

ENSG00000143228 ∙ NCBI:83540 ∙ OMIM:611772 ∙ HGNC:14621 ∙ Uniprot:Q9BZD4 ∙ 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 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		21	1		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)
1-163326094-G-T		not specified	Uncertain significance (May 01, 2024)
1-163326142-C-G		not specified	Uncertain significance (Nov 21, 2022)
1-163328253-A-G		not specified	Uncertain significance (Jun 11, 2024)
1-163328868-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-163328869-G-A		not specified	Uncertain significance (Aug 08, 2022)
1-163336760-G-C		not specified	Uncertain significance (Dec 15, 2022)
1-163336784-T-G		Short stature;Microcephaly	Pathogenic (Dec 22, 2020)
1-163336816-C-T		not specified	Uncertain significance (Oct 13, 2021)
1-163336817-G-A		not specified	Uncertain significance (Feb 28, 2024)
1-163336836-T-G		not specified	Uncertain significance (Sep 29, 2022)
1-163338030-C-T		not specified	Likely benign (Dec 13, 2023)
1-163338034-C-A		not specified	Uncertain significance (Aug 13, 2021)
1-163339467-A-C		not specified	Uncertain significance (Apr 07, 2022)
1-163343845-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-163345778-T-C		4p partial monosomy syndrome	Uncertain significance (-)
1-163347765-C-G		not specified	Uncertain significance (Jan 23, 2024)
1-163347798-G-C		not specified	Uncertain significance (Nov 13, 2023)
1-163347853-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-163348963-A-C		not specified	Uncertain significance (Mar 23, 2022)
1-163348974-G-T		not specified	Uncertain significance (Aug 14, 2023)
1-163355367-G-C		not specified	Uncertain significance (Nov 01, 2022)
1-163355383-A-G		not specified	Uncertain significance (Feb 17, 2024)
1-163355398-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-163355453-T-G		not specified	Uncertain significance (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUF2	protein_coding	protein_coding	ENST00000271452	13	89189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000382	0.998	125625	0	94	125719	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	173	232	0.747	0.0000118	3073
Missense in Polyphen		40	57.535	0.69523		781
Synonymous	0.865	71	80.9	0.878	0.00000434	776
Loss of Function	2.71	12	27.3	0.440	0.00000131	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00112	0.00111
European (Non-Finnish)	0.000503	0.000501
Middle Eastern	0.000381	0.000381
South Asian	0.0000327	0.0000327
Other	0.000329	0.000326

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

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

Mouse Genome Informatics

• Gene name: Nuf2

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