Genetic Variant TAS1R3:p.Cys757Gly (chr1-1334174-T-G) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_152228.3(TAS1R3):c.2269T>G(p.Cys757Gly) 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. 17/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 35)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TAS1R3
NM_152228.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.360

Publications

38 publications found

Variant links:

Genes affected

TAS1R3 (HGNC:15661): (taste 1 receptor member 3) The protein encoded by this gene is a G-protein coupled receptor involved in taste responses. The encoded protein can form a heterodimeric receptor with TAS1R1 to elicit the umami taste response, or it can bind with TAS1R2 to form a receptor for the sweet taste response. [provided by RefSeq, Nov 2015]

TAS1R3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.09812769).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAS1R3	NM_152228.3 link	c.2269T>G	p.Cys757Gly	missense_variant	Exon 6 of 6	ENST00000339381.6	NP_689414.2	Q7RTX0
TAS1R3	XM_017002435.2 link	c.2395T>G	p.Cys799Gly	missense_variant	Exon 5 of 5		XP_016857924.1
TAS1R3	XM_017002436.2 link	c.2392T>G	p.Cys798Gly	missense_variant	Exon 5 of 5		XP_016857925.1
TAS1R3	XM_047431571.1 link	c.2266T>G	p.Cys756Gly	missense_variant	Exon 6 of 6		XP_047287527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAS1R3	ENST00000339381.6 link	c.2269T>G	p.Cys757Gly	missense_variant	Exon 6 of 6	2	NM_152228.3	ENSP00000344411.5		Q7RTX0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1441790

Hom.:

Cov.:

104

AF XY:

0.00

AC XY:

AN XY:

715672

African (AFR)

AF:

0.00

AC:

AN:

33176

American (AMR)

AF:

0.00

AC:

AN:

41666

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25720

East Asian (EAS)

AF:

0.00

AC:

AN:

38660

South Asian (SAS)

AF:

0.00

AC:

AN:

83904

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50698

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5748

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1102600

Other (OTH)

AF:

0.00

AC:

AN:

59618

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.051

BayesDel_addAF

Benign

-0.049

BayesDel_noAF

Benign

-0.31

CADD

Benign

6.5

(source)

DANN

Benign

0.63

DEOGEN2

Benign

0.088

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.31

M_CAP

Benign

0.045

MetaRNN

Benign

0.098

MetaSVM

Benign

-0.82

MutationAssessor

Benign

-0.55

PhyloP100

0.36

PrimateAI

Benign

0.28

PROVEAN

Benign

1.5

REVEL

Benign

0.14

Sift

Uncertain

0.024

Sift4G

Benign

0.080

Polyphen

0.0040

Vest4

0.13

MutPred

0.42

Gain of disorder (P = 9e-04);

MVP

0.13

ClinPred

0.19

GERP RS

-0.84

Varity_R

0.29

gMVP

0.34

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over