TMEM65

protein-coding

transmembrane 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

NM_194291.3

Inheritance

AR

ClinVar variants

U:28B:6

Top phenotype

TMEM65-related disorder

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr8:124,306,189-124,372,701

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~66.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mitochondrial diseaseLIMITED

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).

mitochondrial diseaseMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0044970

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TMEM65 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 23
not providedTotal: 4
TMEM65-related disorderTotal: 2
See casesTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
3
missense
23
clinvar
3
clinvar
26
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
5
clinvar
5
Total00286034
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_194291.3RefSeqNP_919267.27MANE Select
ENST00000297632.8EnsemblENSP00000297632.67MANE Select
ENST00000704783.1EnsemblENSP00000516032.16Standard
ENST00000704785.1EnsemblENSP00000516033.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
tmem65Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.385896.20.6030.000004651505
Missense (PolyPhen)1837.0960.48523516
Synonymous0.1253434.90.9730.00000178507
Loss of Function1.9139.290.3233.92e-7132

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000670.000059rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian00.0absent
Other0.000200.00017rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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