TMEM250
protein-codingtransmembrane protein 250
Gene summary
Involved in positive regulation of cell population proliferation and positive regulation of viral process. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- C9orf69
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.3 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 TMEM250 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152833.3. 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 | 0 | |||||
| missense | 2 | 2 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 0 | 2 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_690046.3 | 1 | MANE Select | |
| Ensembl | ENSP00000453019.1 | 1 | MANE Select | |
| RefSeq | NP_001243455.1 | 1 | Standard | |
| Ensembl | ENSP00000455849.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of cell population proliferation
- viral process
- positive regulation of viral process
- cytoskeleton-dependent cytokinesis
Molecular Function
- GTPase activity
- protein binding
- protein-containing complex scaffold activity
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- septin ring
- microtubule cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000418388
- Coding exons
- 1
- Length
- 4305
- Individuals with no LoFs
- 123868
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 123883
- p
- 0.0000605
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.03 | 78 | 108 | 0.722 | 0.00000859 | 865 |
| Missense (PolyPhen) | 26 | 35.099 | 0.74076 | 311 | ||
| Synonymous | -1.98 | 72 | 53.6 | 1.34 | 0.00000428 | 323 |
| Loss of Function | 0.990 | 1 | 2.78 | 0.360 | 1.19e-7 | 27 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00020 | 0.00020 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000081 | 0.000080 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00017 | 0.00017 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in cell proliferation by promoting progression into S phase. {ECO:0000269|PubMed:21667337}.;