TIMM22
protein-codingtranslocase of inner mitochondrial membrane 22, the group of Tim17 family|TIM22 complex
Gene summary
Multipass transmembrane proteins are brought into mitochondria and inserted into the mitochondrial inner membrane by way of the TIM22 complex. This complex has six subunits and is a twin-pore translocase. The protein encoded by this gene is a subunit of TIM22 and represents the voltage-activated and signal-gated channel. [provided by RefSeq, Jul 2016]
- TEX4
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0030017
Submitter: Ambry Genetics
Inheritance Pattern: Unknown
Disease ID:MONDO:0030017
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0030017
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *TIMM22* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of July 29, 2024. The *TIMM22* gene encodes translocase of inner mitochondrial membrane 22, an essential component of the TIM22 complex. This complex acts as the voltage-activated and signal-gated twin pore and mediates the import and insertion of multipass proteins into the inner mitochondrial membrane. The first and only report of *TIMM22* in relation to autosomal recessive primary mitochondrial disease was in 2018 (PMID: 30452684). *TIMM22* has been associated with a single disease entity to date, combined oxidative phosphorylation deficiency 43 [OMIM# 618851]. This is one disease entity according to the ClinGen Lumping and Splitting Framework, and is considered a primary mitochondrial disease. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included two unique variants (one stop gain variant although nonsense mediated decay is not expected as the premature stop occurs within first 100 base pairs; one missense variant) identified in one case from one publication (PMID: 30452684). Of note, the missense variant is present in population databases including in the homozygous state, so it is hypothesized this is a hypomorphic allele given the extensive functional validation performed in fibroblasts from the single case report. The single reported case had intrauterine growth restriction, low birth weight and length, reduced spontaneous movements, feeding difficulty, gastroesophageal reflux with vomiting, delayed myelination, and elevated blood lactate and creatine kinase. The mechanism of disease is loss of function. This gene-disease relationship is also supported by a biochemical function shared with other genes associated with primary mitochondrial disease (PMID: 33340416). In summary, there is limited evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing evidence has emerged that contradicts the gene-disease relationship. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on July 29, 2024 (SOP Version 10).
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Neurologic
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TIMM22 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013337.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 4 | 5 | |||
| missense | 32 | 3 | 35 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 1 | 0 | 34 | 7 | 0 | 42 |
Highest pathogenic variant AF is 0.000024645415
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037469.2 | 4 | MANE Select | |
| Ensembl | ENSP00000320236.2 | 4 | MANE Select | |
| Ensembl | ENSP00000527860.1 | 2 | Standard | |
| Ensembl | ENSP00000527860.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of proteins
- Mitochondrial protein import
Biological Process
- protein targeting to mitochondrion
- protein insertion into mitochondrial inner membrane
Molecular Function
- protein binding
- protein transmembrane transporter activity
- mitochondrion targeting sequence binding
Cellular Component
- mitochondrial inner membrane
- integral component of membrane
- TIM22 mitochondrial import inner membrane insertion complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000327158
- Coding exons
- 4
- Length
- 6555
- Individuals with no LoFs
- 125715
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 33
- Defined
- 125748
- p
- 0.000131
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.220 | 125 | 118 | 1.06 | 0.00000614 | 1241 |
| Missense (PolyPhen) | 31 | 40.456 | 0.76627 | 400 | ||
| Synonymous | -0.466 | 50 | 46.0 | 1.09 | 0.00000246 | 402 |
| Loss of Function | 0.252 | 7 | 7.76 | 0.902 | 3.26e-7 | 99 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.00039 | 0.00039 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential core component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. In the TIM22 complex, it constitutes the voltage-activated and signal-gated channel. Forms a twin-pore translocase that uses the membrane potential as external driving force in 2 voltage-dependent steps (By similarity). {ECO:0000250|UniProtKB:Q12328}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.694
- RVIS EVS
- 0.1
- RVIS percentile EVS
- 61.49
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.687
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |