MZT1

mitotic spindle organizing protein 1

Basic information

Region (hg38): 13:72708367-72727629

Previous symbols: [ "C13orf37" ]

Links

ENSG00000204899 ∙ NCBI:440145 ∙ OMIM:613448 ∙ HGNC:33830 ∙ Uniprot:Q08AG7 ∙ 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 MZT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MZT1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in MZT1

This is a list of pathogenic ClinVar variants found in the MZT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-72710326-C-T		not specified	Uncertain significance (May 03, 2023)
13-72718960-C-T		not specified	Uncertain significance (Jul 25, 2023)
13-72719035-C-T		not specified	Uncertain significance (Apr 20, 2024)
13-72719076-A-G		not specified	Uncertain significance (Aug 23, 2021)
13-72727536-C-T		not specified	Uncertain significance (Mar 06, 2023)
13-72727595-C-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MZT1	protein_coding	protein_coding	ENST00000377818	3	19331

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0460	0.690	125735	0	4	125739	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.202	44	47.9	0.918	0.00000250	514
Missense in Polyphen		10	12.309	0.81239		167
Synonymous	0.475	15	17.5	0.856	9.13e-7	163
Loss of Function	0.590	2	3.13	0.640	1.30e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.0000203	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000179	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for gamma-tubulin complex recruitment to the centrosome. {ECO:0000269|PubMed:20360068}.
• Pathway: Recruitment of mitotic centrosome proteins and complexes;Centrosome maturation;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.701
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mzt1

Gene ontology

• Biological process: gamma-tubulin complex localization;microtubule nucleation by interphase microtubule organizing center;mitotic spindle assembly
• Cellular component: centrosome;spindle;cytosol;gamma-tubulin ring complex;interphase microtubule organizing center
• Molecular function: protein binding