19-45669567-G-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000164.4(GIPR):​c.47G>A​(p.Cys16Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000042 in 1,428,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000042 ( 0 hom. )

Consequence

GIPR
NM_000164.4 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.558
Variant links:
Genes affected
GIPR (HGNC:4271): (gastric inhibitory polypeptide receptor) This gene encodes a G-protein coupled receptor for gastric inhibitory polypeptide (GIP), which was originally identified as an activity in gut extracts that inhibited gastric acid secretion and gastrin release, but subsequently was demonstrated to stimulate insulin release in the presence of elevated glucose. Mice lacking this gene exhibit higher blood glucose levels with impaired initial insulin response after oral glucose load. Defect in this gene thus may contribute to the pathogenesis of diabetes. [provided by RefSeq, Oct 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.06376889).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GIPRNM_000164.4 linkuse as main transcriptc.47G>A p.Cys16Tyr missense_variant 2/14 ENST00000590918.6 NP_000155.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GIPRENST00000590918.6 linkuse as main transcriptc.47G>A p.Cys16Tyr missense_variant 2/141 NM_000164.4 ENSP00000467494 P2P48546-1

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD3 exomes
AF:
0.0000100
AC:
2
AN:
199116
Hom.:
0
AF XY:
0.00000934
AC XY:
1
AN XY:
107108
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000227
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000420
AC:
6
AN:
1428842
Hom.:
0
Cov.:
31
AF XY:
0.00000282
AC XY:
2
AN XY:
708094
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:
0.00000182
Gnomad4 OTH exome
AF:
0.0000676
GnomAD4 genome
Cov.:
30
Alfa
AF:
0.000102
Hom.:
0
Bravo
AF:
0.00000756

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 submitterclinical testingAmbry GeneticsFeb 16, 2023The c.47G>A (p.C16Y) alteration is located in exon 2 (coding exon 1) of the GIPR gene. This alteration results from a G to A substitution at nucleotide position 47, causing the cysteine (C) at amino acid position 16 to be replaced by a tyrosine (Y). 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
0.068
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
15
DANN
Benign
0.86
DEOGEN2
Benign
0.090
T;.;.
Eigen
Benign
-0.96
Eigen_PC
Benign
-0.91
FATHMM_MKL
Benign
0.32
N
LIST_S2
Benign
0.41
T;T;T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.064
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.34
N;N;N
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Uncertain
0.55
T
PROVEAN
Benign
0.12
.;N;N
REVEL
Benign
0.084
Sift
Benign
0.16
.;T;T
Sift4G
Benign
0.34
T;T;T
Polyphen
0.0
B;B;.
Vest4
0.20
MutPred
0.47
Gain of MoRF binding (P = 0.1222);Gain of MoRF binding (P = 0.1222);Gain of MoRF binding (P = 0.1222);
MVP
0.31
MPC
0.41
ClinPred
0.041
T
GERP RS
1.6
Varity_R
0.074
gMVP
0.62

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs1326368872; hg19: chr19-46172825; API