HGNC Approved Gene Symbol: GLRA2
Cytogenetic location: Xp22.2 Genomic coordinates (GRCh38): X:14,448,779-14,731,812 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xp22.2 | Intellectual developmental disorder, X-linked syndromic, Pilorge type | 301076 | X-linked | 3 |
The GLRA2 gene encodes the alpha-2 subunit of the glycine receptor. The alpha-1 subunit is encoded by the GLRA1 gene (138491), which maps to chromosome 5q32. The GLRA2 gene is expressed in fetal brain and spinal cord, and the GLRA1 gene is expressed predominantly in adult brain and spinal cord (Monani and Burghes, 1996).
Grenningloh et al. (1987) cloned and sequenced cDNAs of the strychnine-binding subunit of the rat glycine receptor, a neurotransmitter-gated chloride channel protein of the central nervous system. They found that the deduced polypeptide shows significant structural and amino acid sequence homology with nicotinic acetylcholine receptor proteins, indicating that they belong to a family of genes encoding neurotransmitter-gated ion channels.
Grenningloh et al. (1990) isolated 2 cDNAs encoding variants (alpha-1 and alpha-2) of the strychnine-binding subunit of the inhibitory glycine receptor from a human fetal brain cDNA library.
Using immunolabeling, Avila et al. (2013) showed that Glra2 was expressed by embryonic mouse cortical interneurons. Glra2 was homogeneously distributed over the surface of the soma and growth cone-like structures of interneurons migrating out of the medial ganglionic eminence. Further analysis confirmed that Glra2 integrated into functional glycine receptors in interneurons.
Using immunostaining, immunofluorescence, and RT-PCR analyses, Lin et al. (2017) showed that Glra2 was expressed in mouse and rat hippocampal adult neural stem cells (ANSCs).
Monani and Burghes (1996) determined that the GLRA2 gene contains 9 exons varying in size from 68 bp to 581 bp. They found that structures of the alpha-subunit glycine receptor gene in humans are very similar to each other and to the alpha-subunit genes in mice.
Cummings et al. (1998) found that GLRA2 has a putative alternatively spliced exon 3.
Using RT-PCR and RNase protection assays, Jensen et al. (2000) detected a decrease in utilization of Glra2 exon 3A in Nova1 (602157)-null mice.
Using a panel of rodent-human cell lines, Grenningloh et al. (1990) mapped the GLRA2 gene to chromosome Xp22.1-p21.2.
In 4 large North Carolina kindreds with X-linked hypophosphatemic rickets (HYP; 307800), Econs et al. (1990) found linkage to a polymorphic probe derived from the 5-prime untranslated portion of the human glycine receptor gene. The maximum lod score was 7.91 at theta = 0.07. Multipoint analysis indicated that GLRA2 is on the telomeric side of HYP.
Gross (2022) mapped the GLRA2 gene to chromosome Xp22.2 based on an alignment of the GLRA2 sequence (GenBank BC032864) with the genomic sequence (GRCh38).
Derry and Barnard (1991) mapped the Glra2 gene of the mouse to the telomeric portion of the X chromosome by backcross analysis of a Mus musculus/Mus spretus interspecies cross.
Using loss- and gain-of-function experiments, Avila et al. (2013) demonstrated that Glra2 expression levels correlated with migration of mouse cortical interneurons. Glycine receptor blockade reduced the migration velocity of cortical interneurons by modulating nucleokinesis. Migration of cortical interneurons was impaired in Glra2 -/- mice, confirming the contribution Glra2-containing glycine receptors to cortical interneuron migration in vivo. Glycine was the main endogenous agonist acting on interneurons during corticogenesis, and interneuron migration was controlled by endogenous glycine-mediated calcium oscillations. Activation of Glra2-containing glycine receptors by endogenous glycine in cortical interneurons controlled migration velocity and nucleokinesis by triggering a molecular pathway that tuned myosin II (see 160775) activity and actomyosin contractility behind the nucleus.
Lin et al. (2017) found that pharmacologic inhibition of Glra2 expression decreased the proliferation of ANSCs both in vitro and in vivo.
By quantitative RT-PCR analysis, Comhair et al. (2018) showed that Glra2 was highly expressed in medium spiny neurons (MSNs) in brains of 1-week-old mice, but was downregulated during postnatal development, and did not generate tonic or phasic glycinergic current in MSNs at postnatal day (P) 7.
X-linked Syndromic Intellectual Developmental Disorder, Pilorge Type
Pilorge et al. (2016) reported 3 different hemizygous mutations in the GLRA2 gene (305990.0001-305990.0003) in 3 male patients with the Pilorge type of X-linked syndromic intellectual developmental disorder (MRXSP; 301076). The patients were ascertained from large cohorts of males with autism spectrum disorder who underwent genetic analysis. There were 2 missense variants and 1 small intragenic deletion. Two mutations occurred de novo and the third was inherited from an unaffected mother. In vitro functional expression studies showed that the mutations interfered with GLRA2 localization and/or function, resulting in absent or impaired glycine receptor activation, which is consistent with a loss of function. The overall findings supported a role for glycinergic transmission in neurocognitive development. No other pathogenic GLRA2 mutations were identified in over 4,000 males with autism spectrum disorder or other neurodevelopmental disorders, suggesting that they are very rare events.
In a girl with MRXSP, Piton et al. (2011) identified a heterozygous missense mutation in the GLRA2 gene (R350L; 305990.0004). The patient was ascertained from a cohort of 142 patients with autism spectrum disorder who underwent direct sequencing of 111 X-linked synaptic genes, including GLRA2. Clinical findings included autism, loss of acquired words, seizures, mild motor developmental delay, macrocephaly, and hypothyroidism. The variant was inherited from the patient's unaffected mother; X-inactivation studies were not performed. Zhang et al. (2017) performed detailed electrophysiologic studies in HEK293 cells, which showed that the R350L mutation caused altered glycine receptor channel properties and kinetics, with increased inhibitory postsynaptic current (IPSC) rise and decay times. The slowed decay times, longer duration of active periods, and increased conductance of the mutant channel indicated that the mutation results in a gain-of-function effect.
In 8 unrelated females (patients 1-8) with MRXSP, Marcogliese et al. (2022) identified de novo heterozygous missense mutations in the GLRA2 gene. Six patients carried the same variant in the GLRA2 gene (T296M; 305990.0005). The mutations, which were found by exome sequencing, were not present in the gnomAD database. Functional studies were performed only for the T296M variant. Marcogliese et al. (2022) found that expression of T296M at high levels caused lethality in Drosophila, whereas low levels of T296M expression caused the formation of melanized nodules in the thorax. Electroretinogram studies in mutant Drosophila suggested that the T296M variant increases synaptic transmission when expressed in postsynaptic neurons, but not at presynaptic neurons. These findings suggested that T296M may act as a gain-of-function allele. Studies of patient cells were not performed. Marcogliese et al. (2022) also identified 5 different hemizygous missense variants (see, e.g., R252C; 305990.0006) in 5 unrelated male patients with MRXSP. All were maternally inherited: 4 of the mothers were unaffected, whereas 1 mother with skewed X inactivation (60:40) was mildly affected. Functional studies were performed only for the R252C variant. Viability studies in mutant Drosophila indicated that the R252C variant was a loss-of-function allele. Electroretinogram studies in mutant flies suggested that the R252C variant decreases synaptic transmission when expressed in synaptic neurons, further suggesting that it causes a loss of GLRA2 function. Studies of patient cells were not performed. The authors concluded that the recurrent de novo T296M mutation in females acts as a gain-of-function allele and that the rare GLRA2 variants found in males behave as loss-of-function alleles.
Polymorphism
Siddique et al. (1989) demonstrated 3 RFLPs of the gene for the 48-kD polypeptide of the human glycine receptor. X-linked transmission was shown in 3 separate families with no male-to-male transmission in 8 informative matings. The genes for the 58-kD and 93-kD proteins that make up the glycine receptor appear to be coded by autosomes.
Young-Pearse et al. (2006) found that Glra2 -/- mice were born at the expected mendelian ratio and were healthy and fertile, with no gross behavioral or morphologic phenotypes. Glra2 -/- mice exhibited normal spinal cord development and morphology. As expected, Glra2 -/- mice lacked developmental electrophysiologic responses to glycine and taurine in cortex. However, wildtype and Glra2 -/- cortices were morphologically indistinguishable, indicating that Glra2 activity is not necessary for normal cortical development. Furthermore, retinal development and function appeared normal in Glra2 -/- mice.
Pilorge et al. (2016) found that morpholino knockdown of the glra2 ortholog in zebrafish led to hyperbranching of spinal motor axons compared to controls. These abnormalities could be rescued by expression of the wildtype gene, but not by mutations found in humans. Glra2-null mice had no abnormalities in social behavior, but showed short and long-term learning and memory deficits for novel objects; spatial learning was similar to wildtype. This was associated with impaired long-term potentiation in vitro in cortical slices from Glra2-null mice. These findings suggested that defective glycinergic signaling results in abnormal plasticity in the prefrontal cortex, a region implicated in autism spectrum disorder.
Lin et al. (2017) found that Glra2 -/y mice had impaired adult hippocampal neurogenesis (AHN) due to inhibition of proliferation of ANSCs in the dentate gyrus (DG). This phenotype was accompanied by deficits in spatial memory.
Comhair et al. (2018) found that deletion of Glra2 in mice severely affected the shape of action potentials and impaired spontaneous activity and the frequency of miniature receptor-mediated currents in MSNs, resulting in behavioral changes in neonatal mice. In adult Glra2-knockout mice, the glutamatergic synapses in MSNs remained functionally underdeveloped. The number of glutamatergic synapses and release probability at presynaptic site was not affected by Glra2 deletion, but the number of postsynaptic receptors was decreased. This deficit was a consequence of impaired development of the neuronal circuitry, since acute blockage of Glra2 expression by an inhibitor in adult MSNs did not affect the properties of glutamatergic synapses.
In a male with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Pilorge et al. (2016) reported a de novo hemizygous c.407A-G transition (chrX:14,599,441, GRCh37) in the GLRA2 gene, resulting in an asn136-to-ser (N136S) substitution at a highly conserved residue in the ligand-binding domain. In vitro functional expression studies in CHO cells showed that the mutation reduced GLRA2 surface expression and glycine sensitivity, consistent with a loss of function. The patient was originally part of a large cohort of over 2,500 simplex families with autism spectrum disorder who underwent whole-exome sequencing.
In Drosophila viability studies, Marcogliese et al. (2022) found that the N136S variant acts as a loss-of-function allele. Further studies in mutant flies also suggested that the N136S variant acted as loss-of-function allele, causing decreased synaptic transmission in electroretinograms.
In a man (patient 1) with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Pilorge et al. (2016) identified a hemizygous 151-kb intragenic deletion (chrX.14,692,533-14,843,587del, GRCh37) in the GLRA2 gene, resulting in the deletion of the last 2 exons (8 and 9). The mutation was inherited from his unaffected mother, consistent with X-linked recessive transmission; her cells showed normal nonskewed X chromosome inactivation. The mutation was predicted to result in loss of transmembrane domains TM3 and TM4. Analysis of patient cells showed that the mutant transcript escaped nonsense-mediated mRNA decay and produced a mutant product that would terminate with 5 additional amino acids followed by a stop codon. In vitro functional expression studies in CHO cells showed that mutant GLRA2 was undetectable at the cell surface and mislocalized to the cytoplasm. There was no current response to glycine, consistent with a loss of function. Expression of the mutation was also unable to rescue abnormal hyperbranching of spinal motor axons in glra2-null zebrafish. The patient was ascertained from a cohort of 996 individuals with autism spectrum disorder who underwent genomewide CNV analysis.
In a man (patient 2) with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Pilorge et al. (2016) identified a de novo hemizygous c.458G-A transition (c.458G-A, NM_002063.3) in the GLRA2 gene, resulting in an arg153-to-gln (R153Q) substitution at a highly conserved residue in the N-terminal extracellular domain. The mutation was absent from the dbSNP (build 138), 1000 Genomes Project, and Exome Variant Server databases. In vitro functional functional expression studies in CHO cells showed that the R153Q mutant induced a 56% decrease in cell surface expression compared to wildtype; overall levels of mutant GLRA2 were decreased, suggesting increased degradation. Further studies demonstrated a dramatically reduced sensitivity to glycine, suggesting that the receptors are unlikely to be significantly activated. Expression of the mutation was also unable to rescue abnormal hyperbranching of spinal motor axons in glra2-null zebrafish. These findings were consistent with a loss of function. The patient was ascertained from a cohort of 400 males with autism spectrum disorder who underwent direct sequencing of the GLRA2 gene; this was the only patient with a mutation.
In a girl with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Piton et al. (2011) identified a heterozygous c.1049G-T transversion in the GLRA2 gene, resulting in an arg350-to-leu (R350L) substitution. The patient was ascertained from a cohort of 142 patients with autism spectrum disorder who underwent direct sequencing of 111 X-linked synaptic genes, including GLRA2. The variant was inherited from the patient's unaffected mother; X-inactivation studies were not performed.
Variant Function
Through detailed electrophysiologic studies in HEK293 cells, Zhang et al. (2017) showed that the R350L mutation caused altered glycine receptor channel properties and kinetics, with increased inhibitory postsynaptic current (IPSC) rise and decay times. The slowed decay times, longer duration of active periods, and increased conductance of the mutant channel indicated that the R350L mutation results in a gain-of-function effect. Clinical findings included loss of acquired words, seizures, mild motor developmental delay, macrocephaly, and hypothyroidism. Zhang et al. (2017) noted that the R350L variant (c.1049G-T, NM_001118885) is numbered R323L in the protein lacking the signal peptide.
In 6 unrelated females (patients 1-6) with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Marcogliese et al. (2022) identified a de novo heterozygous c.887C-T transition (c.887C-T, NM_001118886.1) in the GLRA2 gene, resulting in a thr296-to-met (T296M) substitution. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Marcogliese et al. (2022) found that high expression levels of T296M caused lethality in Drosophila, whereas low levels of T296M expression caused the formation of melanized nodules in the thorax. Electroretinogram studies in mutant Drosophila suggested that the T296M variant increases synaptic transmission when expressed in postsynaptic neurons, but not at presynaptic neurons. These findings suggested that T296M may act as a gain-of-function allele. Studies of patient cells were not performed.
In an 11-month-old boy (patient 9) with Pilorge type X-linked syndromic intellectual developmental disorder (MRXSP; 301076), Marcogliese et al. (2022) identified a hemizygous c.754C-T transition (c.754C-T, NM_001118886.1) in the GLRA2 gene, resulting in an arg252-to-cys (R252C) substitution. The mutation, which was found by whole-exome sequencing, was inherited from the unaffected mother. Her cells showed skewed X inactivation (82%). The variant was found once in a female in the gnomAD database. Viability studies in mutant Drosophila indicated that the R252C variant was a loss-of-function allele. Electroretinogram studies in mutant flies suggested that the R252C variant decreases synaptic transmission when expressed in synaptic neurons, further suggesting that it causes a loss of GLRA2 function.
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