TIMMDC1
Basic information
Region (hg38): 3:119498547-119525090
Previous symbols: [ "C3orf1" ]
Links
Phenotypes
GenCC
Source:
- mitochondrial complex I deficiency, nuclear type 31 (Moderate), mode of inheritance: AR
- mitochondrial complex I deficiency (Supportive), mode of inheritance: AR
- mitochondrial complex I deficiency, nuclear type 31 (Strong), mode of inheritance: AR
- Leigh syndrome (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Mitochondrial complex I deficiency, nuclear type 31 | 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 | Audiologic/Otolaryngologic; Biochemical; Neurologic | 28604674 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (62 variants)
- not_specified (47 variants)
- Mitochondrial_complex_I_deficiency,_nuclear_type_31 (13 variants)
- TIMMDC1-related_disorder (5 variants)
- Mitochondrial_complex_I_deficiency,_nuclear_type_1 (5 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TIMMDC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016589.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 11 | 13 | ||||
missense | 64 | 70 | ||||
nonsense | 5 | |||||
start loss | 1 | 1 | ||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
Total | 0 | 9 | 71 | 14 | 2 |
Highest pathogenic variant AF is 0.00010511102
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TIMMDC1 | protein_coding | protein_coding | ENST00000494664 | 7 | 26559 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.11e-8 | 0.334 | 125702 | 0 | 45 | 125747 | 0.000179 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.00439 | 156 | 156 | 0.999 | 0.00000800 | 1827 |
Missense in Polyphen | 40 | 49.659 | 0.80549 | 560 | ||
Synonymous | -1.01 | 67 | 57.3 | 1.17 | 0.00000278 | 573 |
Loss of Function | 0.726 | 14 | 17.3 | 0.811 | 9.79e-7 | 177 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000279 | 0.000275 |
Ashkenazi Jewish | 0.000200 | 0.000198 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000231 | 0.000229 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000397 | 0.000392 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chaperone protein involved in the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex (complex I). Participates in constructing the membrane arm of complex I. {ECO:0000269|PubMed:24191001}.;
- Pathway
- Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Complex I biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
(Consensus)
Recessive Scores
- pRec
- 0.0658
Intolerance Scores
- loftool
- rvis_EVS
- 0.35
- rvis_percentile_EVS
- 74.37
Haploinsufficiency Scores
- pHI
- 0.0207
- hipred
- N
- hipred_score
- 0.144
- ghis
- 0.450
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- 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
- Timmdc1
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype;
Gene ontology
- Biological process
- mitochondrial respiratory chain complex I assembly
- Cellular component
- nucleus;nucleoplasm;mitochondrion;mitochondrial inner membrane;integral component of membrane
- Molecular function
- protein binding