MZT2A

mitotic spindle organizing protein 2A, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 2:131464899-131492743

Previous symbols: [ "FAM128A" ]

Links

ENSG00000173272 ∙ NCBI:653784 ∙ OMIM:613449 ∙ HGNC:33187 ∙ Uniprot:Q6P582 ∙ 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 MZT2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MZT2A 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in MZT2A

This is a list of pathogenic ClinVar variants found in the MZT2A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-131478155-T-G			Likely benign (Mar 29, 2018)
2-131478185-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-131478191-C-T		Keratoconus 9	Pathogenic (Apr 04, 2018)
2-131478261-G-A		not specified	Uncertain significance (Jun 02, 2024)
2-131478293-G-A		not specified	Uncertain significance (May 16, 2024)
2-131478299-G-A		not specified	Uncertain significance (Feb 14, 2023)
2-131478318-T-C		not specified	Uncertain significance (Nov 22, 2021)
2-131478358-G-GTT		Keratoconus 9	Pathogenic (May 08, 2018)
2-131479347-C-T		not specified	Uncertain significance (Dec 17, 2023)
2-131479390-C-T			Likely benign (Dec 31, 2019)
2-131479422-T-A			Benign (Dec 31, 2019)
2-131480123-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-131480159-C-T		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
2-131480160-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-131480285-T-C		not specified	Uncertain significance (Nov 17, 2023)
2-131480291-T-C		not specified	Uncertain significance (Jun 21, 2023)
2-131480330-T-C		not specified	Uncertain significance (Dec 11, 2023)
2-131480333-C-T		not specified	Uncertain significance (Mar 31, 2024)
2-131480336-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-131480349-T-C		not specified	Uncertain significance (Oct 27, 2022)
2-131480361-C-A		not specified	Uncertain significance (Feb 27, 2023)
2-131480409-C-T		not specified	Uncertain significance (May 26, 2024)
2-131480451-C-T		not specified	Uncertain significance (Sep 29, 2022)
2-131480492-T-A		not specified	Uncertain significance (Jun 07, 2024)
2-131480542-C-T			Likely benign (Jan 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MZT2A	protein_coding	protein_coding	ENST00000309451	3	27844

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000800	0.0960	125013	0	5	125018	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.301	93	85.2	1.09	0.00000465	978
Missense in Polyphen		28	24.991	1.1204		327
Synonymous	-0.515	45	40.8	1.10	0.00000248	350
Loss of Function	-1.69	6	2.89	2.07	1.23e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000200	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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)

Haploinsufficiency Scores

• pHI: 0.0993
• hipred: N
• hipred_score: 0.112
• ghis: 0.479

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mzt2

Gene ontology

• Cellular component: nucleoplasm;centrosome;spindle;cytosol;gamma-tubulin ring complex