TMEM168
protein-codingtransmembrane protein 168
Gene summary
Enables sodium channel regulator activity. Predicted to act upstream of or within regulation of ubiquitin-dependent protein catabolic process and regulation of voltage-gated sodium channel activity. Located in nuclear membrane and transport vesicle. [provided by Alliance of Genome Resources, Apr 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015263
Submitter: ClinGen
The relationship between TMEM168 and autosomal dominant Brugada syndrome was suggested by Shimizu et al. in 2020, following the identification of the TMEM168 c.1616G>A, p.Arg539Gln variant in a family with Brugada syndrome (PMID: 32175648). Functional evidence from mouse and cell models suggested a mechanism involving decreased cardiomyocyte cell surface Nav1.5 expression in cells with the p.Arg539Gln variant. In a follow-up publication, Nguyen et al. suggested that the TMEM168 p.Arg539Gln variant was involved in sequestering αB-crystallin, thereby promoting Nav1.5 degradation (PMID: 34086898). However, with an allele frequency of 9.88 x 10-5 in the South Asian population (and 1.24 x 10-5 overall in gnomAD v4.1) this variant is too common to be a monogenic driver of autosomal dominant Brugada syndrome. As of the date of this classification, there are no further reports of TMEM168 variants causing cardiac disease in the literature. This gene-disease relationship was evaluated on January 13, 2026, by the Hereditary Cardiovascular Disorders GCEP. Given the absence of compelling clinical genetic data, this gene-disease classification was disputed. This classification was approved by the ClinGen Hereditary Cardiovascular Disorders GCEP on January 13, 2026 (in accordance with SOP Version 11).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TMEM168 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022484.6. 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 | 1 | ||||
| missense | 86 | 1 | 1 | 88 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 87 | 1 | 1 | 89 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071929.3 | 4 | MANE Select | |
| Ensembl | ENSP00000323068.4 | 4 | MANE Select | |
| RefSeq | NP_001274426.1 | 4 | Standard | |
| Ensembl | ENSP00000404253.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- integral component of membrane
- transport vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312814
- Coding exons
- 4
- Length
- 28211
- Individuals with no LoFs
- 125677
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 70
- Defined
- 125747
- p
- 0.000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.890 | 325 | 373 | 0.870 | 0.0000193 | 4552 |
| Missense (PolyPhen) | 92 | 113.29 | 0.81209 | 1358 | ||
| Synonymous | -0.813 | 147 | 135 | 1.09 | 0.00000702 | 1375 |
| Loss of Function | 2.80 | 8 | 22.2 | 0.360 | 9.30e-7 | 334 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.00046 | 0.00046 | rare |
| Other | 0.00021 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.234
- RVIS EVS
- -0.62
- RVIS percentile EVS
- 17.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.584
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |