GLRA4

glycine receptor alpha 4 (pseudogene), the group of Glycine receptors

Basic information

Region (hg38): X:103707224-103728203

Links

ENSG00000188828 ∙ NCBI:441509 ∙ ∙ HGNC:31715 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GLRA4 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1	7	10
Total	0	0	2	1	7

Variants in GLRA4

This is a list of pathogenic ClinVar variants found in the GLRA4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-103707365-C-A			Benign (Dec 31, 2019)
X-103707415-T-C			Benign (Dec 31, 2019)
X-103707440-A-G			Benign (Dec 31, 2019)
X-103707507-T-C			Benign (Dec 31, 2019)
X-103712280-G-A		not specified	Uncertain significance (Feb 27, 2025)
X-103712335-A-G		not specified	Likely benign (Jun 28, 2024)
X-103713526-T-C			Likely benign (Feb 25, 2018)
X-103713612-C-T			Uncertain significance (Mar 01, 2019)
X-103713616-C-T		not specified	Uncertain significance (Mar 04, 2024)
X-103713618-C-A		not specified	Uncertain significance (Mar 04, 2024)
X-103713633-C-A		not specified	Uncertain significance (Apr 25, 2023)
X-103713648-C-T			Likely benign (Dec 31, 2019)
X-103713649-G-T		not specified	Uncertain significance (Aug 28, 2024)
X-103713661-G-A		not specified	Likely benign (May 15, 2023)
X-103713691-C-G		not specified	Uncertain significance (Dec 15, 2023)
X-103713698-C-A		not specified	Uncertain significance (Jun 17, 2024)
X-103713715-C-T		not specified	Uncertain significance (Sep 17, 2021)
X-103713741-C-T		not specified	Uncertain significance (Apr 08, 2024)
X-103713802-C-A			Likely benign (-)
X-103713810-G-A		not specified	Uncertain significance (Jan 18, 2025)
X-103713849-G-A		not specified	Uncertain significance (Oct 13, 2023)
X-103719107-C-T			Benign (Dec 31, 2019)
X-103719170-A-G			Uncertain significance (Mar 01, 2023)
X-103719191-G-A			Benign (Dec 31, 2019)
X-103719233-G-T			Likely benign (Oct 17, 2017)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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

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