ZWINT

ZW10 interacting kinetochore protein, the group of KNL1 complex

Basic information

Region (hg38): 10:56357227-56361273

Links

ENSG00000122952 ∙ ∙ OMIM:609177 ∙ HGNC:13195 ∙ Uniprot:O95229 ∙ 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 ZWINT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZWINT 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					1	1
missense			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	22	1	1

Variants in ZWINT

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

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

Position	Type	Phenotype	Significance	ClinVar
10-56358444-G-A		not specified	Uncertain significance (Oct 13, 2023)
10-56358454-A-G			Benign (Apr 04, 2018)
10-56358593-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-56358605-T-C		not specified	Uncertain significance (Dec 01, 2022)
10-56358623-T-G		not specified	Uncertain significance (Nov 16, 2021)
10-56358629-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-56358655-C-G		not specified	Uncertain significance (Mar 19, 2024)
10-56358659-G-A		not specified	Uncertain significance (Jun 10, 2022)
10-56358808-T-C		not specified	Uncertain significance (Jul 06, 2021)
10-56358824-C-T		not specified	Uncertain significance (Mar 06, 2023)
10-56358870-G-C		not specified	Likely benign (Oct 02, 2023)
10-56358895-T-G		not specified	Uncertain significance (Jun 23, 2021)
10-56358898-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-56358925-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-56359518-C-T		not specified	Uncertain significance (Jun 24, 2022)
10-56359679-G-A			Benign (Apr 04, 2018)
10-56359697-A-G		not specified	Uncertain significance (May 16, 2023)
10-56359709-G-A		not specified	Uncertain significance (Mar 22, 2023)
10-56359727-C-G		not specified	Uncertain significance (Jun 05, 2023)
10-56359785-C-A		not specified	Uncertain significance (Mar 24, 2023)
10-56359842-T-C		not specified	Uncertain significance (Jul 12, 2023)
10-56359853-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-56360052-C-G		not specified	Uncertain significance (Jul 25, 2023)
10-56360068-T-A		not specified	Uncertain significance (Jan 07, 2022)
10-56360314-C-A		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZWINT	protein_coding	protein_coding	ENST00000373944	8	4048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.27e-11	0.137	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.502	166	149	1.12	0.00000772	1800
Missense in Polyphen		42	46.493	0.90337		630
Synonymous	0.291	55	57.8	0.951	0.00000294	532
Loss of Function	0.507	17	19.4	0.876	0.00000108	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the MIS12 complex, which is required for kinetochore formation and spindle checkpoint activity. Required to target ZW10 to the kinetochore at prometaphase. {ECO:0000269|PubMed:15094189, ECO:0000269|PubMed:15485811, ECO:0000269|PubMed:15824131, ECO:0000269|PubMed:16732327}.
• 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: 0.106

Intolerance Scores

• loftool: 0.976
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.95

Haploinsufficiency Scores

• pHI: 0.521
• hipred: Y
• hipred_score: 0.518
• ghis: 0.628

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.620

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zwint

Gene ontology

• Biological process: mitotic sister chromatid segregation;mitotic cell cycle checkpoint;cell division;establishment of localization in cell
• Cellular component: kinetochore;condensed chromosome kinetochore;nucleus;nucleoplasm;cytoplasm;cytosol;nuclear body;dendrite
• Molecular function: protein binding;protein N-terminus binding