MICOS13

mitochondrial contact site and cristae organizing system subunit 13, the group of Mitochondrial contact site and cristae organizing system subunits

Basic information

Region (hg38): 19:5678420-5680516

Previous symbols: [ "C19orf70" ]

Links

ENSG00000174917 ∙ NCBI:125988 ∙ OMIM:616658 ∙ HGNC:33702 ∙ Uniprot:Q5XKP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 3-methylglutaconic aciduria type 3 (Supportive), mode of inheritance: AR
• mitochondrial disease (Definitive), 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
Combined oxidative phosphorylation deficiency 37	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	Biochemical; Cardiovascular; Neurologic; Ophthalmologic	27623147; 29618761; 27485409

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MICOS13 gene.

• not provided (14 variants)
• Combined oxidative phosphorylation deficiency 37 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICOS13 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				4		4
missense			1			1
nonsense						0
start loss			1			1
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			1	1	1	3
non coding				2		2
Total	1	1	2	6	0

Highest pathogenic variant AF is 0.00000660

Variants in MICOS13

This is a list of pathogenic ClinVar variants found in the MICOS13 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-5678594-T-C		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
19-5678601-G-C		Inborn genetic diseases	Uncertain significance (Jan 12, 2022)
19-5678617-C-T			Likely benign (Apr 28, 2022)
19-5678620-C-T			Likely benign (Dec 11, 2023)
19-5678646-T-C			Likely benign (Mar 01, 2024)
19-5678647-GC-G			Conflicting classifications of pathogenicity (Jul 27, 2023)
19-5678650-T-C		Combined oxidative phosphorylation deficiency 37	Pathogenic (Nov 01, 2019)
19-5678663-C-T			Likely benign (Oct 24, 2022)
19-5679338-G-T			Likely benign (Oct 24, 2022)
19-5679399-G-T			Uncertain significance (Jul 06, 2022)
19-5679401-GAA-G		MICOS13-related disorder	Benign/Likely benign (Dec 11, 2023)
19-5679416-A-C			Likely benign (Nov 12, 2022)
19-5679567-C-T			Likely benign (Nov 17, 2023)
19-5679642-CG-C			Likely pathogenic (Dec 22, 2021)
19-5679646-G-C			Likely benign (Jan 31, 2023)
19-5679657-C-T			Uncertain significance (Jun 21, 2022)
19-5679715-G-T		Inborn genetic diseases	Likely pathogenic (Aug 27, 2021)
19-5679718-C-T			Likely benign (Jul 15, 2022)
19-5679730-G-A			Likely benign (Jan 12, 2024)
19-5679739-A-T		MICOS13-related disorder	Likely benign (Jul 13, 2022)
19-5679743-A-G			Uncertain significance (Oct 03, 2023)
19-5679748-TC-T		Mitochondrial hepato-encephalopathy • Combined oxidative phosphorylation deficiency 37	Conflicting classifications of pathogenicity (Feb 22, 2019)
19-5679764-C-T		Combined oxidative phosphorylation deficiency 37	Pathogenic (Feb 22, 2019)
19-5680090-G-A		MICOS13-related disorder	Likely benign (Oct 27, 2022)
19-5680439-C-T			Likely benign (Nov 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICOS13	protein_coding	protein_coding	ENST00000309324	4	2476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000834	0.568	125512	0	7	125519	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.102	69	66.7	1.04	0.00000381	744
Missense in Polyphen		13	16.922	0.76821		216
Synonymous	0.532	26	29.7	0.876	0.00000190	234
Loss of Function	0.430	5	6.15	0.813	2.64e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000543	0.0000529
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Constituent of mature MICOS complex, it is required for the formation of cristae junction (CJ) and maintenance of cristae morphology. Required for the incorporation of MINOS1/MIC10 into the MICOS complex. {ECO:0000269|PubMed:25997101}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.671
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.571

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 2410015M20Rik