RAET1G
protein-codingretinoic acid early transcript 1G
Gene summary
This gene encodes a member of the major histocompatibility complex (MHC) class I family of proteins. Although the encoded protein includes C-terminal transmembrane and cytoplasmic domains, proteolytic processing results in the removal of these domains and subsequent tethering to the plasma membrane by a glycosylphosphatidylinositol (GPI)-anchor. The encoded protein is one of several related ligands of the natural killer group 2, member D (NKG2D) receptor, which functions as an activating receptor in innate and adaptive immunity. This gene is present in a gene cluster on chromosome 6. [provided by RefSeq, Jul 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.2 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 RAET1G variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001001788.4. 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 | 44 | 3 | 47 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 47 | 3 | 0 | 50 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001001788.2 | 5 | MANE Select | |
| Ensembl | ENSP00000356329.2 | 5 | MANE Select | |
| Ensembl | ENSP00000356330.2 | 4 | Standard | |
| Ensembl | ENSP00000417503.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Natural killer cell mediated cytotoxicity - Homo sapiens (human)
- Post-translational modification: synthesis of GPI-anchored proteins
- Post-translational protein modification
- Metabolism of proteins
Biological Process
- T cell mediated cytotoxicity
- positive regulation of natural killer cell cytokine production
- immune response
- viral process
- natural killer cell activation
Molecular Function
- protein binding
- natural killer cell lectin-like receptor binding
Cellular Component
- extracellular region
- extracellular space
- endoplasmic reticulum
- plasma membrane
- external side of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367360
- Coding exons
- 5
- Length
- 6244
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125741
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.325 | 189 | 177 | 1.07 | 0.00000944 | 2150 |
| Missense (PolyPhen) | 43 | 46.806 | 0.91868 | 665 | ||
| Synonymous | -1.73 | 88 | 69.6 | 1.26 | 0.00000421 | 673 |
| Loss of Function | 0.639 | 9 | 11.3 | 0.795 | 4.92e-7 | 135 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000044 | 0.000044 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Isoform 1: Binds and activates the KLRK1/NKG2D receptor, mediating natural killer cell cytotoxicity. {ECO:0000269|PubMed:15240696, ECO:0000269|PubMed:18544572, ECO:0000269|PubMed:19658097}.; FUNCTION: Isoform 2: Stimulates natural killer cells to secrete IFNG. {ECO:0000269|PubMed:18544572}.;
Recessive Scores
- pRec
- 0.0540
Intolerance Scores
- LoFtool
- 0.707
- RVIS EVS
- 1.91
- RVIS percentile EVS
- 97.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0455
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |