NUF2
Basic information
Region (hg38): 1:163266576-163355764
Previous symbols: [ "CDCA1" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 21 | 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:
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:
- 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
- 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