NM_152232.6:c.1987A>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152232.6(TAS1R2):​c.1987A>G​(p.Ser663Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S663T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

TAS1R2
NM_152232.6 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.37
Variant links:
Genes affected
TAS1R2 (HGNC:14905): (taste 1 receptor member 2) Contributes to sweet taste receptor activity. Involved in detection of chemical stimulus involved in sensory perception of sweet taste and positive regulation of cytokinesis. Part of sweet taste receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.15876037).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAS1R2NM_152232.6 linkc.1987A>G p.Ser663Gly missense_variant Exon 6 of 6 ENST00000375371.4 NP_689418.2 Q8TE23

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAS1R2ENST00000375371.4 linkc.1987A>G p.Ser663Gly missense_variant Exon 6 of 6 2 NM_152232.6 ENSP00000364520.3 Q8TE23

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
38
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Mar 08, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.1987A>G (p.S663G) alteration is located in exon 6 (coding exon 6) of the TAS1R2 gene. This alteration results from a A to G substitution at nucleotide position 1987, causing the serine (S) at amino acid position 663 to be replaced by a glycine (G). 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
0.067
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
10
DANN
Benign
0.97
DEOGEN2
Benign
0.22
T
Eigen
Benign
-0.90
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.045
N
LIST_S2
Benign
0.81
T
M_CAP
Uncertain
0.15
D
MetaRNN
Benign
0.16
T
MetaSVM
Benign
-0.42
T
MutationAssessor
Benign
1.6
L
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-1.8
N
REVEL
Uncertain
0.43
Sift
Uncertain
0.028
D
Sift4G
Benign
0.17
T
Polyphen
0.39
B
Vest4
0.11
MutPred
0.48
Gain of helix (P = 0.0425);
MVP
0.24
MPC
0.25
ClinPred
0.25
T
GERP RS
-10
Varity_R
0.29
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: chr1-19166626; API