X-137030577-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4

The NM_054021.2(GPR101):​c.1098C>A​(p.Asp366Glu) 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. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 22)

Consequence

GPR101
NM_054021.2 missense

Scores

1
1
15

Clinical Significance

Pathogenic no assertion criteria provided P:1O:1

Conservation

PhyloP100: 0.312
Variant links:
Genes affected
GPR101 (HGNC:14963): (G protein-coupled receptor 101) The protein encoded by this gene is an orphan G protein-coupled receptor of unknown function. The encoded protein is a member of a family of proteins that contain seven transmembrane domains and transduce extracellular signals through heterotrimeric G proteins. [provided by RefSeq, Sep 2011]

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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;
PP5
Variant X-137030577-G-T is Pathogenic according to our data. Variant chrX-137030577-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 192259.Status of the report is no_assertion_criteria_provided, 0 stars.
BP4
Computational evidence support a benign effect (MetaRNN=0.17194661). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPR101NM_054021.2 linkuse as main transcriptc.1098C>A p.Asp366Glu missense_variant 2/2 ENST00000651716.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPR101ENST00000651716.2 linkuse as main transcriptc.1098C>A p.Asp366Glu missense_variant 2/2 NM_054021.2 P1
ENST00000693626.2 linkuse as main transcriptn.394-29948G>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Pituitary adenoma, growth hormone-secreting, 2 Pathogenic:1Other:1
not provided, no classification providedliterature onlyGeneReviews-- -
Pathogenic, no assertion criteria providedliterature onlyOMIMMar 26, 2015- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.68
CADD
Benign
13
DANN
Uncertain
0.98
DEOGEN2
Benign
0.0023
T
FATHMM_MKL
Benign
0.068
N
LIST_S2
Benign
0.49
T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.17
T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.9
L
MutationTaster
Benign
1.0
N
PrimateAI
Benign
0.48
T
PROVEAN
Benign
-0.26
N
REVEL
Benign
0.10
Sift
Benign
0.045
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.66
P
Vest4
0.20
MutPred
0.30
Loss of glycosylation at S363 (P = 0.1387);
MVP
0.61
MPC
1.3
ClinPred
0.59
D
GERP RS
-0.080
Varity_R
0.081

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1556379508; hg19: chrX-136112736; API