TMIGD1
protein-codingtransmembrane and immunoglobulin domain containing 1, the group of I-set domain containing
Gene summary
Predicted to enable cell adhesion mediator activity and protein homodimerization activity. Involved in several processes, including negative regulation of apoptotic process; regulation of cell migration; and regulation of membrane permeability. Acts upstream of or within intestinal epithelial cell migration; negative regulation of epithelial cell proliferation; and regulation of protein kinase activity. Located in adherens junction; cytoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- TMIGD
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.7 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 TMIGD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_206832.3. 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 | 36 | 6 | 42 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 6 | 0 | 42 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_996663.1 | 6 | MANE Select | |
| Ensembl | ENSP00000332404.4 | 6 | MANE Select | |
| RefSeq | NP_001306871.1 | 4 | Standard | |
| Ensembl | ENSP00000446118.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of cell migration
- regulation of cell population proliferation
- negative regulation of apoptotic process
- regulation of membrane permeability
Cellular Component
- cytoplasm
- plasma membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000328886
- Coding exons
- 6
- Length
- 17727
- Individuals with no LoFs
- 125681
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 65
- Defined
- 125746
- p
- 0.000258
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.732 | 164 | 140 | 1.17 | 0.00000714 | 1736 |
| Missense (PolyPhen) | 50 | 45.609 | 1.0963 | 610 | ||
| Synonymous | 0.478 | 48 | 52.4 | 0.916 | 0.00000302 | 489 |
| Loss of Function | 0.376 | 11 | 12.4 | 0.885 | 6.13e-7 | 152 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00058 | 0.00058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00032 | 0.00032 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May control cell-cell adhesion, cell migration and proliferation, cell morphology, and protects renal epithelial cells from oxidative cell injury to promote cell survival. {ECO:0000269|PubMed:26342724}.;
Intolerance Scores
- LoFtool
- 0.745
- RVIS EVS
- -0.09
- RVIS percentile EVS
- 46.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00309
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |