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): 19:5678421-5680516

Previous symbols: [ "C19orf70" ]

Links

ENSG00000174917NCBI:125988OMIM:616658HGNC:33702Uniprot:Q5XKP0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Combined oxidative phosphorylation deficiency 37ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingBiochemical; Cardiovascular; Neurologic; Ophthalmologic27623147; 29618761; 27485409

ClinVar

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

  • not provided (1 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
6
clinvar
6
missense
4
clinvar
1
clinvar
5
nonsense
1
clinvar
1
start loss
1
clinvar
1
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
2
3
non coding
5
clinvar
5
Total 1 2 5 12 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)3126313
19-5678601-G-C Inborn genetic diseases Uncertain significance (Jan 12, 2022)3126312
19-5678617-C-T Likely benign (Apr 28, 2022)2171050
19-5678620-C-T Likely benign (Dec 11, 2023)2415537
19-5678646-T-C Likely benign (Mar 01, 2024)3067289
19-5678647-GC-G Conflicting classifications of pathogenicity (Mar 19, 2024)1007450
19-5678650-T-C Combined oxidative phosphorylation deficiency 37 Pathogenic (Nov 01, 2019)425157
19-5678663-C-T Likely benign (Oct 24, 2022)1682905
19-5679338-G-T Likely benign (Oct 24, 2022)2071883
19-5679399-G-T Uncertain significance (Jul 06, 2022)2190629
19-5679401-GAA-G MICOS13-related disorder Benign (Dec 11, 2023)2065825
19-5679416-A-C Likely benign (Nov 12, 2022)2783395
19-5679567-C-T Likely benign (Nov 17, 2023)2962000
19-5679642-CG-C Combined oxidative phosphorylation deficiency 37 Conflicting classifications of pathogenicity (Feb 09, 2024)1526386
19-5679646-G-C Likely benign (Jan 31, 2023)3006557
19-5679657-C-T Uncertain significance (Jun 21, 2022)2007490
19-5679715-G-T Inborn genetic diseases Likely pathogenic (Aug 27, 2021)3126314
19-5679718-C-T Likely benign (Jul 15, 2022)1948114
19-5679730-G-A Likely benign (Jan 12, 2024)2710373
19-5679739-A-T MICOS13-related disorder Likely benign (Jul 13, 2022)3032293
19-5679743-A-G Uncertain significance (Oct 03, 2023)2851815
19-5679748-TC-T Mitochondrial hepato-encephalopathy • Combined oxidative phosphorylation deficiency 37 Conflicting classifications of pathogenicity (Feb 22, 2019)617631
19-5679764-C-T Combined oxidative phosphorylation deficiency 37 Pathogenic (Feb 22, 2019)619099
19-5680090-G-A MICOS13-related disorder Likely benign (Oct 27, 2022)3047453
19-5680439-C-T Likely benign (Nov 01, 2023)1932086

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MICOS13protein_codingprotein_codingENST00000309324 42476
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0008340.568125512071255190.0000279
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1026966.71.040.00000381744
Missense in Polyphen1316.9220.76821216
Synonymous0.5322629.70.8760.00000190234
Loss of Function0.43056.150.8132.64e-764

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006200.0000616
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00005430.0000529
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

pHI
hipred
N
hipred_score
0.170
ghis
0.571

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
K
gene_indispensability_pred
gene_indispensability_score

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
2410015M20Rik
Phenotype