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GeneBe

14-52268642-G-A

Variant summary

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

The NM_000953.3(PTGDR):c.828G>A(p.Met276Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000209 in 1,432,246 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: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

PTGDR
NM_000953.3 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.05
Variant links:
Genes affected
PTGDR (HGNC:9591): (prostaglandin D2 receptor) This gene encodes a member of the guanine nucleotide-binding protein (G protein)-coupled receptor (GPCR) superfamily. The receptors are seven-pass transmembrane proteins that respond to extracellular cues and activate intracellular signal transduction pathways. This protein is reported to be a receptor for prostaglandin D2, which is a mediator of allergic inflammation and allergic airway inflammation in asthma. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

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=0.15963405).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PTGDRNM_000953.3 linkuse as main transcriptc.828G>A p.Met276Ile missense_variant 1/2 ENST00000306051.3
PTGDRNM_001281469.2 linkuse as main transcriptc.828G>A p.Met276Ile missense_variant 1/3
PTGDRXM_005267891.5 linkuse as main transcriptc.828G>A p.Met276Ile missense_variant 1/3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PTGDRENST00000306051.3 linkuse as main transcriptc.828G>A p.Met276Ile missense_variant 1/21 NM_000953.3 P1Q13258-1
PTGDRENST00000553372.1 linkuse as main transcriptc.828G>A p.Met276Ile missense_variant 1/33 Q13258-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000209
AC:
3
AN:
1432246
Hom.:
0
Cov.:
31
AF XY:
0.00000282
AC XY:
2
AN XY:
709154
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:
0.00000274
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

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

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2024PTGDR: PM2, BP4 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
Cadd
Benign
18
Dann
Benign
0.89
DEOGEN2
Benign
0.059
T;.
Eigen
Benign
-0.59
Eigen_PC
Benign
-0.38
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.65
T;T
M_CAP
Benign
0.0034
T
MetaRNN
Benign
0.16
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.045
N;N
MutationTaster
Benign
0.54
N;N
PrimateAI
Benign
0.37
T
PROVEAN
Benign
1.1
N;N
REVEL
Benign
0.075
Sift
Benign
0.69
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0030
B;.
Vest4
0.21
MutPred
0.48
Loss of catalytic residue at M276 (P = 0.0821);Loss of catalytic residue at M276 (P = 0.0821);
MVP
0.26
MPC
0.36
ClinPred
0.25
T
GERP RS
3.5
Varity_R
0.17
gMVP
0.26

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: chr14-52735360; API