TIMMDC1

translocase of inner mitochondrial membrane domain containing 1, the group of Mitochondrial complex I assembly complex|Tim17 family

Basic information

Region (hg38): 3:119498547-119525090

Previous symbols: [ "C3orf1" ]

Links

ENSG00000113845NCBI:51300OMIM:615534HGNC:1321Uniprot:Q9NPL8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Mitochondrial complex I deficiency, nuclear type 31ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Biochemical; Neurologic28604674

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TIMMDC1 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
11
clinvar
1
clinvar
13
missense
2
clinvar
64
clinvar
3
clinvar
1
clinvar
70
nonsense
2
clinvar
3
clinvar
5
start loss
1
1
frameshift
1
clinvar
3
clinvar
4
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total 0 9 71 14 2

Highest pathogenic variant AF is 0.00010511102

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TIMMDC1protein_codingprotein_codingENST00000494664 726559
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.11e-80.3341257020451257470.000179
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.004391561560.9990.000008001827
Missense in Polyphen4049.6590.80549560
Synonymous-1.016757.31.170.00000278573
Loss of Function0.7261417.30.8119.79e-7177

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002790.000275
Ashkenazi Jewish0.0002000.000198
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0002310.000229
Middle Eastern0.000.00
South Asian0.0003970.000392
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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