GLRA4
Basic information
Region (hg38): X:103707224-103728203
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GLRA4 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | 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 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GLRA4 | protein_coding | protein_coding | ENST00000372617 | 9 | 21432 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 9.38e-9 | 0.171 | 125283 | 125 | 339 | 125747 | 0.00185 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.259 | 164 | 174 | 0.945 | 0.0000144 | 2729 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0336 | 0.0256 |
| Ashkenazi Jewish | 0.000135 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000195 | 0.000132 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000648 | 0.000359 |
| Other | 0.00114 | 0.000815 |
dbNSFP
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}.;
- Pathway
- Neuronal System;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses
(Consensus)
Recessive Scores
- pRec
- 0.0999
Intolerance Scores
- loftool
- 0.474
- rvis_EVS
- 1.17
- rvis_percentile_EVS
- 92.73
Haploinsufficiency Scores
- pHI
- 0.484
- hipred
- N
- hipred_score
- 0.251
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.177
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Glra4
- Phenotype
Zebrafish Information Network
- Gene name
- glra4a
- Affected structure
- motor neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased functionality
Gene ontology
- Biological process
- signal transduction;neuropeptide signaling pathway;chemical synaptic transmission;ion transmembrane transport;regulation of membrane potential;response to amino acid;nervous system process;synaptic transmission, glycinergic;excitatory postsynaptic potential;chloride transmembrane transport
- Cellular component
- integral component of plasma membrane;cell junction;dendrite;chloride channel complex;neuron projection;perikaryon;synapse;glycinergic synapse;integral component of postsynaptic specialization membrane
- Molecular function
- transmembrane signaling receptor activity;extracellular ligand-gated ion channel activity;chloride channel activity;glycine binding;extracellularly glycine-gated chloride channel activity;transmitter-gated ion channel activity