7-107045028-C-G

Variant summary

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

The ENST00000265717.5(PRKAR2B):​c.121C>G​(p.Gln41Glu) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

PRKAR2B
ENST00000265717.5 missense

Scores

1
1
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.498
Variant links:
Genes affected
PRKAR2B (HGNC:9392): (protein kinase cAMP-dependent type II regulatory subunit beta) cAMP is a signaling molecule important for a variety of cellular functions. cAMP exerts its effects by activating the cAMP-dependent protein kinase, which transduces the signal through phosphorylation of different target proteins. The inactive kinase holoenzyme is a tetramer composed of two regulatory and two catalytic subunits. cAMP causes the dissociation of the inactive holoenzyme into a dimer of regulatory subunits bound to four cAMP and two free monomeric catalytic subunits. Four different regulatory subunits and three catalytic subunits have been identified in humans. The protein encoded by this gene is one of the regulatory subunits. This subunit can be phosphorylated by the activated catalytic subunit. This subunit has been shown to interact with and suppress the transcriptional activity of the cAMP responsive element binding protein 1 (CREB1) in activated T cells. Knockout studies in mice suggest that this subunit may play an important role in regulating energy balance and adiposity. The studies also suggest that this subunit may mediate the gene induction and cataleptic behavior induced by haloperidol. [provided by RefSeq, Jul 2008]

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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=0.057694495).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRKAR2BNM_002736.3 linkuse as main transcriptc.121C>G p.Gln41Glu missense_variant 1/11 ENST00000265717.5 NP_002727.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRKAR2BENST00000265717.5 linkuse as main transcriptc.121C>G p.Gln41Glu missense_variant 1/111 NM_002736.3 ENSP00000265717 P1
PRKAR2BENST00000706580.1 linkuse as main transcriptn.119C>G non_coding_transcript_exon_variant 1/8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32

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 GeneticsApr 07, 2023The c.121C>G (p.Q41E) alteration is located in exon 1 (coding exon 1) of the PRKAR2B gene. This alteration results from a C to G substitution at nucleotide position 121, causing the glutamine (Q) at amino acid position 41 to be replaced by a glutamic acid (E). 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
0.061
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
16
DANN
Benign
0.89
DEOGEN2
Benign
0.20
T
Eigen
Benign
-0.74
Eigen_PC
Benign
-0.51
FATHMM_MKL
Benign
0.52
D
M_CAP
Uncertain
0.17
D
MetaRNN
Benign
0.058
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
-1.5
N
MutationTaster
Benign
0.89
N;N
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
1.1
N
REVEL
Benign
0.11
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.15
MutPred
0.36
Gain of ubiquitination at K46 (P = 0.0483);
MVP
0.38
MPC
0.92
ClinPred
0.11
T
GERP RS
3.0
Varity_R
0.17
gMVP
0.18

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-106685473; API