MSTO1

misato mitochondrial distribution and morphology regulator 1

Basic information

Region (hg38): 1:155563234-155614951

Links

ENSG00000125459 ∙ NCBI:55154 ∙ OMIM:617619 ∙ HGNC:29678 ∙ Uniprot:Q9BUK6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome (Moderate), mode of inheritance: AR
• mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome (Strong), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy, mitochondrial, and ataxia	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic; Ophthalmologic	28544275; 28554942

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MSTO1 gene.

• not provided (81 variants)
• Inborn genetic diseases (32 variants)
• Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome (27 variants)
• not specified (4 variants)
• See cases (2 variants)
• MSTO1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSTO1 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				13	1	14
missense		2	57	8	6	73
nonsense	1	1				2
start loss		1				1
frameshift	1	1	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)	1	2				3
splice region			3	2	2	7
non coding			1	5	10	16
Total	3	7	59	26	17

Highest pathogenic variant AF is 0.0000591

Variants in MSTO1

This is a list of pathogenic ClinVar variants found in the MSTO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155609989-C-T			Benign (May 13, 2021)
1-155610040-C-T			Benign (May 13, 2021)
1-155610044-A-G			Benign (May 13, 2021)
1-155610045-CA-C			Benign (May 13, 2021)
1-155610249-A-C		Inborn genetic diseases	Likely pathogenic (Feb 18, 2021)
1-155610262-C-T		Inborn genetic diseases	Likely benign (Dec 01, 2023)
1-155610270-G-A		Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	Uncertain significance (May 16, 2023)
1-155610282-C-G			Uncertain significance (Jan 25, 2022)
1-155610292-A-G		not specified	Uncertain significance (Apr 23, 2021)
1-155610299-C-G			Likely benign (Apr 01, 2024)
1-155610313-C-A		See cases	Likely pathogenic (Jun 17, 2022)
1-155610327-C-T		Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	Pathogenic (Dec 03, 2020)
1-155610437-G-C		Inborn genetic diseases	Uncertain significance (Aug 17, 2021)
1-155610440-C-T			Pathogenic (Jul 06, 2023)
1-155610453-C-G		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
1-155610461-C-A			Benign (May 04, 2021)
1-155610468-G-C		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
1-155610494-C-A			Uncertain significance (Apr 12, 2023)
1-155610528-A-C		Inborn genetic diseases	Uncertain significance (Feb 18, 2021)
1-155610565-G-C		See cases • Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	Uncertain significance (May 31, 2023)
1-155611080-G-T		Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	Uncertain significance (-)
1-155611098-G-A		Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome	Uncertain significance (Mar 26, 2024)
1-155611218-A-G			Conflicting classifications of pathogenicity (Oct 01, 2023)
1-155611225-G-C		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
1-155611230-C-T		Mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome • Inborn genetic diseases	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSTO1	protein_coding	protein_coding	ENST00000245564	14	138175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.62e-9	0.613	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0211	262	261	1.00	0.0000134	3615
Missense in Polyphen		68	73.619	0.92368		1106
Synonymous	-0.452	116	110	1.05	0.00000589	1197
Loss of Function	1.27	17	23.7	0.717	0.00000109	319

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000161	0.000152
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000108	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of mitochondrial distribution and morphology (PubMed:17349998, PubMed:28554942, PubMed:28544275). Required for mitochondrial fusion and mitochondrial network formation (PubMed:28554942, PubMed:28544275). {ECO:0000269|PubMed:17349998, ECO:0000269|PubMed:28544275, ECO:0000269|PubMed:28554942}.

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.520
• ghis: 0.423

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.288

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msto1

Gene ontology

• Biological process: mitochondrial genome maintenance;mitotic sister chromatid segregation;mitochondrion organization;mitochondrion distribution;mitotic spindle assembly
• Cellular component: cytoplasm;mitochondrial outer membrane
• Molecular function: molecular_function