MICOS13
Basic information
Region (hg38): 19:5678421-5680516
Previous symbols: [ "C19orf70" ]
Links
Phenotypes
GenCC
Source:
- 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:
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
- 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 | |||||
missense | 5 | |||||
nonsense | 1 | |||||
start loss | 1 | |||||
frameshift | 1 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 2 | 3 | |||
non coding | 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) | ||
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:
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- 2410015M20Rik
- Phenotype