11-88508731-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001143831.3(GRM5):​c.3500C>T​(p.Ser1167Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

GRM5
NM_001143831.3 missense

Scores

12
5
2

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.48
Variant links:
Genes affected
GRM5 (HGNC:4597): (glutamate metabotropic receptor 5) This gene encodes a member of the G-protein coupled receptor 3 protein family. The encoded protein is a metabatropic glutamate receptor, whose signaling activates a phosphatidylinositol-calcium second messenger system. This protein may be involved in the regulation of neural network activity and synaptic plasticity. Glutamatergic neurotransmission is involved in most aspects of normal brain function and can be perturbed in many neuropathologic conditions. A pseudogene of this gene has been defined on chromosome 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
GRM5-AS1 (HGNC:40265): (GRM5 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GRM5NM_001143831.3 linkc.3500C>T p.Ser1167Phe missense_variant Exon 10 of 10 ENST00000305447.5 NP_001137303.1 P41594-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GRM5ENST00000305447.5 linkc.3500C>T p.Ser1167Phe missense_variant Exon 10 of 10 1 NM_001143831.3 ENSP00000306138.4 P41594-1
GRM5ENST00000305432.9 linkc.3404C>T p.Ser1135Phe missense_variant Exon 8 of 8 1 ENSP00000305905.5 P41594-2
GRM5ENST00000455756.6 linkc.3404C>T p.Ser1135Phe missense_variant Exon 9 of 9 2 ENSP00000405690.2 P41594-2
GRM5-AS1ENST00000526448.1 linkn.4156G>A non_coding_transcript_exon_variant Exon 1 of 6 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1433024
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
712768
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Oct 22, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.3500C>T (p.S1167F) alteration is located in exon 9 (coding exon 9) of the GRM5 gene. This alteration results from a C to T substitution at nucleotide position 3500, causing the serine (S) at amino acid position 1167 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.96
BayesDel_addAF
Pathogenic
0.40
D
BayesDel_noAF
Pathogenic
0.34
CADD
Pathogenic
31
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.50
.;.;D
Eigen
Pathogenic
0.72
Eigen_PC
Pathogenic
0.71
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
D;.;D
M_CAP
Pathogenic
0.59
D
MetaRNN
Uncertain
0.61
D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Benign
1.9
.;.;L
PrimateAI
Pathogenic
0.87
D
PROVEAN
Uncertain
-3.0
D;D;D
REVEL
Pathogenic
0.80
Sift
Pathogenic
0.0
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
D;D;D
Vest4
0.46
MutPred
0.48
.;.;Gain of catalytic residue at S1167 (P = 0.0018);
MVP
0.80
ClinPred
1.0
D
GERP RS
4.9
Varity_R
0.85
gMVP
0.79

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-88241899; COSMIC: COSV100550243; COSMIC: COSV100550243; API