MZT1

protein-coding

mitotic spindle organizing protein 1

Gene summary

Involved in gamma-tubulin complex localization. Located in centrosome and spindle. Part of gamma-tubulin ring complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C13orf37

MANE transcript

NM_001071775.3

Inheritance

—

ClinVar variants

U:15

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr13:72,708,367-72,727,629

External References & Databases

Ensembl (ENSG00000204899)

Transcript & Mutation Effects

hg38 • Region Span ~19.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MZT1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001071775.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	15	0	0	15

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001071775.3	RefSeq	NP_001065243.1	3	MANE Select
ENST00000377818.4	Ensembl	ENSP00000367049.3	3	MANE Select
ENST00001067900.1	Ensembl	ENSP00000737706.1	3	Standard
ENST00001067903.1	Ensembl	ENSP00000737709.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Recruitment of mitotic centrosome proteins and complexes
Centrosome maturation
G2/M Transition
Mitotic G2-G2/M phases
Recruitment of NuMA to mitotic centrosomes

Biological Process

gamma-tubulin complex localization
microtubule nucleation by interphase microtubule organizing center
mitotic spindle assembly

Molecular Function

protein binding

Cellular Component

centrosome
spindle
cytosol
gamma-tubulin ring complex
interphase microtubule organizing center

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377818
Coding exons: 3
Length: 19331
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125739
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.202	44	47.9	0.918	0.00000250	514
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000020	0.000018	rare
South Asian	0	0.0	absent
Other	0.00018	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for gamma-tubulin complex recruitment to the centrosome. {ECO:0000269|PubMed:20360068}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

RVIS EVS: 0.17
RVIS percentile EVS: 65.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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