GLRA4
pseudoglycine receptor alpha 4 (pseudogene), the group of Glycine receptors
Gene summary
This gene encodes a glycine receptor and member of the ligand-gated ion channel family of proteins. The encoded protein is missing the fourth transmembrane region compared to related proteins in mouse and rat, and experimental data suggests that the human protein is functionally inactive. However, there is strong evidence to support transcription of this gene. As a result, RefSeq, in collaboration with Ensembl-GENCODE, has determined that this locus is best described as a transcribed pseudogene. [provided by RefSeq, Aug 2019]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
GenCC 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 GLRA4 variants in ClinVar
No annotated ClinVar phenotypes.
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 | 0 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| No transcripts match your selected source or search query. | ||||
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| glra4a | Danio rerio | Structure: motor neuron Quality: decreased functionality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neuronal System
- Neurotransmitter receptors and postsynaptic signal transmission
- Transmission across Chemical Synapses
Biological Process
- signal transduction
- neuropeptide signaling pathway
- chemical synaptic transmission
- ion transmembrane transport
- regulation of membrane potential
Molecular Function
- transmembrane signaling receptor activity
- extracellular ligand-gated ion channel activity
- chloride channel activity
- glycine binding
- extracellularly glycine-gated chloride channel activity
Cellular Component
- integral component of plasma membrane
- cell junction
- dendrite
- chloride channel complex
- neuron projection
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000372617
- Coding exons
- 9
- Length
- 21432
- Individuals with no LoFs
- 125283
- Homozygous LoFs
- 125
- Heterozygous LoFs
- 339
- Defined
- 125747
- p
- 0.00185
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.259 | 164 | 174 | 0.945 | 0.0000144 | 2729 |
| Missense (PolyPhen) | 71 | 80.497 | 0.88203 | 1317 | ||
| Synonymous | -0.244 | 67 | 64.5 | 1.04 | 0.00000500 | 827 |
| Loss of Function | 0.288 | 13 | 14.2 | 0.918 | 0.00000111 | 219 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.032 | 0.024 | notable |
| Latino/Admixed American | 0.0018 | 0.0014 | notable |
| Ashkenazi Jewish | 0.00014 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00013 | rare |
| South Asian | 0.00065 | 0.00036 | rare |
| Other | 0.0011 | 0.00081 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Glycine receptors are ligand-gated chloride channels. Channel opening is triggered by extracellular glycine. Channel opening is also triggered by taurine and beta-alanine. Plays a role in the down-regulation of neuronal excitability. Contributes to the generation of inhibitory postsynaptic currents. {ECO:0000250|UniProtKB:Q61603}.;
Recessive Scores
- pRec
- 0.0999
Intolerance Scores
- LoFtool
- 0.474
- RVIS EVS
- 1.17
- RVIS percentile EVS
- 92.73
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.177
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |