TMEM65
protein-codingtransmembrane protein 65
Gene summary
Enables calcium:sodium antiporter activity. Involved in calcium export from the mitochondrion. Located in intercalated disc and plasma membrane. Is active in mitochondrial inner membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~66.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: ClinGen
The relationship between *TMEM65* and primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of July 15, 2024. The *TMEM65* gene encodes transmembrane protein 65 that localizes to inner mitochondrial membrane. However, the exact function of this protein remains uncharacterized. The first and only case report of *TMEM65*-related autosomal recessive primary mitochondrial disease was in 2017 (PMID: 28295037), While various names could be given to the constellation of features seen in those with *TMEM65*-related disorders, pathogenic variants in this gene cause a primary mitochondrial disease. Therefore, the *TMEM65* phenotype has been lumped into one disease entity according to the ClinGen Lumping and Splitting Framework. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included a single homozygous splice site variant in one proband from one publication (PMID: 28295037). This was a girl from a consanguineous family who had intrauterine growth restriction, microcephaly, global developmental delay, developmental regression, seizures, spasticity, and dysmorphic features. Brain imaging showed brain atrophy and signal changes in the white matter, cerebellum, and thalami. Decreased mitochondrial DNA content was noted in skeletal muscle and mitochondrial respiratory chain enzyme analysis in skeletal muscle showed reduced activities of complexes I+III, II+III, and IV. The mechanism of disease is loss of function. This gene-disease association is also supported by functional alteration in patient and non-patient cells, rescue in patient cells, and mouse and zebrafish models (PMIDs: 28295037, 33319071, 36257954, 26403541). 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 15, 2024 (SOP Version 10).
Inheritance Pattern: AR
Disease ID:MONDO:0044970
Submitter: PanelApp Australia
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TMEM65 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194291.3. 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 | 3 | 3 | ||||
| missense | 23 | 3 | 26 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 28 | 6 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919267.2 | 7 | MANE Select | |
| Ensembl | ENSP00000297632.6 | 7 | MANE Select | |
| Ensembl | ENSP00000516032.1 | 6 | Standard | |
| Ensembl | ENSP00000516033.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tmem65 | Danio rerio | Structure: heart Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cardiac ventricle development
- regulation of cardiac conduction
Cellular Component
- mitochondrial inner membrane
- plasma membrane
- intercalated disc
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000297632
- Coding exons
- 7
- Length
- 60703
- Individuals with no LoFs
- 124966
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 124969
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.38 | 58 | 96.2 | 0.603 | 0.00000465 | 1505 |
| Missense (PolyPhen) | 18 | 37.096 | 0.48523 | 516 | ||
| Synonymous | 0.125 | 34 | 34.9 | 0.973 | 0.00000178 | 507 |
| Loss of Function | 1.91 | 3 | 9.29 | 0.323 | 3.92e-7 | 132 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000067 | 0.000059 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00020 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play an important role in cardiac development and function. May regulate cardiac conduction and the function of the gap junction protein GJA1. May contributes to the stability and proper localization of GJA1 to cardiac intercalated disk thereby regulating gap junction communication (By similarity). May also play a role in the regulation of mitochondrial respiration and mitochondrial DNA copy number maintenance (PubMed:28295037). {ECO:0000250|UniProtKB:Q4VAE3, ECO:0000269|PubMed:28295037}.;
Intolerance Scores
- LoFtool
- 0.194
- RVIS EVS
- -0.03
- RVIS percentile EVS
- 51.04
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.192
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |