13-26759183-C-G

Variant summary

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

The NM_005288.4(GPR12):​c.645G>C​(p.Gln215His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,110 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000033 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

GPR12
NM_005288.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.17
Variant links:
Genes affected
GPR12 (HGNC:4466): (G protein-coupled receptor 12) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in adenylate cyclase-activating G protein-coupled receptor signaling pathway and regulation of metabolic process. Predicted to act upstream of or within G protein-coupled receptor signaling pathway and cellular calcium ion homeostasis. Predicted to be integral component of plasma membrane. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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
GPR12NM_005288.4 linkc.645G>C p.Gln215His missense_variant Exon 2 of 2 ENST00000405846.5 NP_005279.1 P47775A8K2F5
GPR12XM_005266360.3 linkc.168G>C p.Gln56His missense_variant Exon 2 of 2 XP_005266417.1 B4DG25

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPR12ENST00000405846.5 linkc.645G>C p.Gln215His missense_variant Exon 2 of 2 1 NM_005288.4 ENSP00000384932.3 P47775
GPR12ENST00000381436.2 linkc.645G>C p.Gln215His missense_variant Exon 1 of 1 6 ENSP00000370844.2 P47775

Frequencies

GnomAD3 genomes
AF:
0.0000330
AC:
5
AN:
151696
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000589
Gnomad OTH
AF:
0.000479
GnomAD4 exome
AF:
0.00000411
AC:
6
AN:
1461414
Hom.:
0
Cov.:
32
AF XY:
0.00000413
AC XY:
3
AN XY:
726994
show subpopulations
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:
0.00000540
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000330
AC:
5
AN:
151696
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
74038
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000589
Gnomad4 OTH
AF:
0.000479
Alfa
AF:
0.0000565
Hom.:
0
Bravo
AF:
0.0000113

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Jan 23, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.645G>C (p.Q215H) alteration is located in exon 2 (coding exon 1) of the GPR12 gene. This alteration results from a G to C substitution at nucleotide position 645, causing the glutamine (Q) at amino acid position 215 to be replaced by a histidine (H). 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
Benign
0.29
BayesDel_addAF
Uncertain
0.043
T
BayesDel_noAF
Benign
-0.18
CADD
Benign
17
DANN
Uncertain
0.99
DEOGEN2
Benign
0.10
T;T
Eigen
Benign
-0.29
Eigen_PC
Benign
-0.13
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.79
.;T
M_CAP
Benign
0.011
T
MetaRNN
Uncertain
0.46
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.86
L;L
PrimateAI
Uncertain
0.69
T
PROVEAN
Benign
-1.1
N;N
REVEL
Benign
0.15
Sift
Benign
0.32
T;T
Sift4G
Benign
0.69
T;T
Polyphen
0.055
B;B
Vest4
0.72
MutPred
0.65
Gain of catalytic residue at Q219 (P = 0.0025);Gain of catalytic residue at Q219 (P = 0.0025);
MVP
0.85
MPC
1.5
ClinPred
0.69
D
GERP RS
3.6
Varity_R
0.19
gMVP
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1159024647; hg19: chr13-27333320; API