TIMM22

protein-coding

translocase 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]

Previous symbols:
  • TEX4

MANE transcript

NM_013337.4

Inheritance

AR

ClinVar variants

P:1U:34B:7

Top phenotype

Combined oxidative phosphorylation deficiency 43

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr17:997,129-1,003,671

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~6.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0044970

Submitter: PanelApp Australia

combined oxidative phosphorylation deficiency 43LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030017

Submitter: Ambry Genetics

combined oxidative phosphorylation deficiency 43LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030017

Submitter: Labcorp Genetics (formerly Invitae)

combined oxidative phosphorylation deficiency 43LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0030017

Submitter: G2P

mitochondrial diseaseLIMITED

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)

Combined oxidative phosphorylation deficiency 43AR

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

Refs: 30452684Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TIMM22 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 30
not providedTotal: 5
TIMM22-related disorderTotal: 2
Combined oxidative phosphorylation deficiency 43Total: 2

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
4
clinvar
5
missense
32
clinvar
3
clinvar
35
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total10347042

Highest pathogenic variant AF is 0.000024645415

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_013337.4RefSeqNP_037469.24MANE Select
ENST00000327158.5EnsemblENSP00000320236.24MANE Select
ENST00000857801.1EnsemblENSP00000527860.12Standard
ENST00000857801.2EnsemblENSP00000527860.12Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.2201251181.060.000006141241
Missense (PolyPhen)3140.4560.76627400
Synonymous-0.4665046.01.090.00000246402
Loss of Function0.25277.760.9023.26e-799

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000890.000088rare
South Asian0.000390.00039rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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