chr1-6555563-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_138697.4(TAS1R1):c.190A>G(p.Arg64Gly) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000431 in 1,392,244 control chromosomes in the GnomAD database, with no homozygous occurrence. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000043 ( 0 hom. )
Consequence
TAS1R1
NM_138697.4 missense, splice_region
NM_138697.4 missense, splice_region
Scores
1
8
10
Splicing: ADA: 0.8553
2
Clinical Significance
Conservation
PhyloP100: 2.57
Genes affected
TAS1R1 (HGNC:14448): (taste 1 receptor member 1) The protein encoded by this gene is a G protein-coupled receptor and is a component of the heterodimeric amino acid taste receptor T1R1+3. The T1R1+3 receptor responds to L-amino acids but not to D-enantiomers or other compounds. Most amino acids that are perceived as sweet activate T1R1+3, and this activation is strictly dependent on an intact T1R1+3 heterodimer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2010]
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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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAS1R1 | NM_138697.4 | c.190A>G | p.Arg64Gly | missense_variant, splice_region_variant | 1/6 | ENST00000333172.11 | |
TAS1R1 | NM_177540.3 | c.190A>G | p.Arg64Gly | missense_variant, splice_region_variant | 1/5 | ||
TAS1R1 | XM_011542206.3 | c.190A>G | p.Arg64Gly | missense_variant, splice_region_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAS1R1 | ENST00000333172.11 | c.190A>G | p.Arg64Gly | missense_variant, splice_region_variant | 1/6 | 1 | NM_138697.4 | P1 | |
TAS1R1 | ENST00000351136.7 | c.190A>G | p.Arg64Gly | missense_variant, splice_region_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
Cov.:
34
GnomAD4 exome AF: 0.00000431 AC: 6AN: 1392244Hom.: 0 Cov.: 30 AF XY: 0.00000292 AC XY: 2AN XY: 685078
GnomAD4 exome
AF:
AC:
6
AN:
1392244
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
685078
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 34
GnomAD4 genome
?
Cov.:
34
Alfa
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.190A>G (p.R64G) alteration is located in exon 1 (coding exon 1) of the TAS1R1 gene. This alteration results from a A to G substitution at nucleotide position 190, causing the arginine (R) at amino acid position 64 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;N
PrimateAI
Benign
T
PROVEAN
Uncertain
N;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
B;D
Vest4
MutPred
Loss of stability (P = 0.0832);Loss of stability (P = 0.0832);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at