TOM1L1
protein-codingtarget of myb1 like 1 membrane trafficking protein
Gene summary
Enables clathrin binding activity and protein kinase binding activity. Involved in negative regulation of mitotic nuclear division; positive regulation of protein phosphorylation; and signal transduction. Located in cytosol and endosome. [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 ~62.6 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 TOM1L1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005486.3. 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 | 70 | 2 | 72 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 74 | 2 | 0 | 76 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005477.2 | 15 | MANE Select | |
| Ensembl | ENSP00000460823.1 | 15 | MANE Select | |
| RefSeq | NP_001308102.1 | 10 | Standard | |
| RefSeq | NP_001308103.1 | 12 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- EGFR1
Biological Process
- intracellular protein transport
- signal transduction
- positive regulation of protein autophosphorylation
- activation of protein kinase activity
- ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
Molecular Function
- protein binding
- SH3 domain binding
- protein kinase binding
- clathrin binding
- protein kinase activator activity
Cellular Component
- cytoplasm
- lysosome
- endosome
- Golgi stack
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000575882
- Coding exons
- 15
- Length
- 62563
- Individuals with no LoFs
- 125649
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 98
- Defined
- 125748
- p
- 0.000394
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.298 | 236 | 249 | 0.947 | 0.0000117 | 3155 |
| Missense (PolyPhen) | 82 | 83.869 | 0.97771 | 1162 | ||
| Synonymous | 1.70 | 69 | 89.5 | 0.771 | 0.00000456 | 875 |
| Loss of Function | 1.64 | 19 | 28.4 | 0.669 | 0.00000139 | 338 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00055 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00066 | 0.00065 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00039 | 0.00039 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Probable adapter protein involved in signaling pathways. Interacts with the SH2 and SH3 domains of various signaling proteins when it is phosphorylated. May promote FYN activation, possibly by disrupting intramolecular SH3-dependent interactions (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0938
Intolerance Scores
- LoFtool
- 0.914
- RVIS EVS
- -0.69
- RVIS percentile EVS
- 15.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.643
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |