chrX-123184537-T-C

Position:

• chrX-123184537-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 8P and 5B. PVS1 BS1_Supporting BS2

The NM_000828.5(GRIA3):​c.2T>C​(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000147 in 1,090,266 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 20)
  • Exomes 𝑓: 0.000015 (0 hom. 6 hem.)
• Consequence: GRIA3 NM_000828.5 start_lost
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:4
• Conservation: PhyloP100: 0.295

Genes affected

GRIA3 (HGNC:4573): (glutamate ionotropic receptor AMPA type subunit 3) Glutamate receptors are the predominant excitatory neurotransmitter receptors in the mammalian brain and are activated in a variety of normal neurophysiologic processes. These receptors are heteromeric protein complexes composed of multiple subunits, arranged to form ligand-gated ion channels. The classification of glutamate receptors is based on their activation by different pharmacologic agonists. The subunit encoded by this gene belongs to a family of AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate)-sensitive glutamate receptors, and is subject to RNA editing (AGA->GGA; R->G). Alternative splicing at this locus results in different isoforms, which may vary in their signal transduction properties. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PVS1: Start lost variant, no new inframe start found.
• BS1: Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0000147 (16/1090266) while in subpopulation MID AF= 0.000486 (2/4115). AF 95% confidence interval is 0.0000855. There are 0 homozygotes in gnomad4_exome. There are 6 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High Hemizygotes in GnomAdExome4 at 6 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRIA3	NM_000828.5	c.2T>C	p.Met1?	start_lost	1/16	ENST00000622768.5	NP_000819.4
GRIA3	NM_007325.5	c.2T>C	p.Met1?	start_lost	1/16	ENST00000620443.2	NP_015564.5
GRIA3	NM_001256743.2	c.2T>C	p.Met1?	start_lost	1/4		NP_001243672.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIA3	ENST00000620443.2	c.2T>C	p.Met1?	start_lost	1/16	1	NM_007325.5	ENSP00000478489	P4
GRIA3	ENST00000622768.5	c.2T>C	p.Met1?	start_lost	1/16	5	NM_000828.5	ENSP00000481554	A1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD3 exomes AF: 0.0000273 AC: 5 AN: 183430 Hom.: 0 AF XY: 0.0000295 AC XY: 2 AN XY: 67906

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000611

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000147 AC: 16 AN: 1090266 Hom.: 0 Cov.: 29 AF XY: 0.0000168 AC XY: 6 AN XY: 356216

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000120

Gnomad4 OTH exome AF: 0.0000874

GnomAD4 genome Cov.: 20

Alfa AF: 0.000223 Hom.: 0

ExAC AF: 0.0000494 AC: 6

EpiCase AF: 0.0000546

EpiControl AF: 0.000119

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2018	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 24, 2024	This sequence change affects the initiator methionine of the GRIA3 mRNA. The next in-frame methionine is located at codon 7. This variant is present in population databases (rs752728469, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with GRIA3-related conditions. ClinVar contains an entry for this variant (Variation ID: 624438). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 22, 2022	Initiation codon variant in a gene for which loss-of-function is not a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 34426522, 28152038) -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 07, 2014

The p.M1? pathogenic mutation (also known as c.2T>C), located in coding exon 1 of the GRIA3 gene, results from a T to C substitution at nucleotide position 2. This alters the methionine residue at the native initiation codon. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples with coverage at this position. Sequence variations that modify the initiation codon (ATG) are expected to cause a shift in the mRNA reading frame and possibly absence of protein translation. However, this amino acid position is not well conserved and a number of species do not have the initiation codon at this position. Furthermore, another ATG that is highly conserved among species is located down stream. The ATG sequence, located six amino acids down stream from the human reference sequence, is purported to function as the start site for rat GluR3 based on cDNA studies (Rampersad, V et al. Biochim Biophys Acta 1994;1219:563-6). In humans, iontropic flutamate receptors (iGluR) are purported to contain a short signal peptide (between 14-33 amino acids long) at the N-terminus that targets the protein to the cell membrane and mislocalization may disuprt neuronal function (Traynelis SF, Pharmacol. Rev. 2010 Sep; 62(3):405-96). It is anticipated that the p.M1? alteration, would result in the shortening of the signal peptide and lead to mislocalization of the hGluR3 protein; however direct evidence on this alteration's affect on transport to the cell membrane is unavailable. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Benign	-0.68
CADD	Benign	19
DANN	Benign	0.97
DEOGEN2	Benign	0.079	T;T;T;T;T;.
FATHMM_MKL	Benign	0.43	N
LIST_S2	Uncertain	0.90	.;D;D;D;.;D
M_CAP	Benign	0.035	D
MetaRNN	Uncertain	0.60	D;D;D;D;D;D
MetaSVM	Benign	-1.1	T
MutationTaster	Benign	1.0	N;N;N;N;N;N
PROVEAN	Benign	-0.45	.;.;.;.;N;.
Sift	Pathogenic	0.0	.;.;.;.;D;.
Sift4G	Pathogenic	0.0	D;.;D;D;.;D
Polyphen		0.0	.;B;.;.;B;B
Vest4		0.26
MutPred		0.96		Gain of phosphorylation at M1 (P = 0.0331);Gain of phosphorylation at M1 (P = 0.0331);Gain of phosphorylation at M1 (P = 0.0331);Gain of phosphorylation at M1 (P = 0.0331);Gain of phosphorylation at M1 (P = 0.0331);Gain of phosphorylation at M1 (P = 0.0331);
MVP		0.21
ClinPred		0.22	T
GERP RS		2.9
Varity_R		0.62
gMVP		0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs752728469; hg19: chrX-122318389;