TMEM209
protein-codingtransmembrane protein 209
Gene summary
Predicted to be located in Golgi apparatus and nuclear envelope. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TMEM209 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_032842.4. 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 | 1 | ||||
| missense | 55 | 1 | 56 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 62 | 1 | 0 | 63 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_116231.2 | 15 | MANE Select | |
| Ensembl | ENSP00000380747.2 | 15 | MANE Select | |
| RefSeq | NP_001288092.1 | 14 | Standard | |
| RefSeq | NP_001350407.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000397622
- Coding exons
- 15
- Length
- 43056
- Individuals with no LoFs
- 123066
- Homozygous LoFs
- 11
- Heterozygous LoFs
- 1578
- Defined
- 124655
- p
- 0.00639
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.746 | 268 | 305 | 0.880 | 0.0000156 | 3659 |
| Missense (PolyPhen) | 62 | 96.42 | 0.64302 | 1236 | ||
| Synonymous | 0.530 | 103 | 110 | 0.936 | 0.00000633 | 1059 |
| Loss of Function | 1.53 | 24 | 33.6 | 0.715 | 0.00000178 | 394 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.0024 | 0.0023 | notable |
| Ashkenazi Jewish | 0.0020 | 0.0020 | notable |
| East Asian | 0.00045 | 0.00045 | rare |
| Finnish | 0.011 | 0.011 | notable |
| European (Non-Finnish) | 0.0053 | 0.0053 | notable |
| South Asian | 0.020 | 0.019 | notable |
| Other | 0.0069 | 0.0068 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.798
- RVIS EVS
- 0
- RVIS percentile EVS
- 53.85
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.765
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |