19-39415048-A-G

Variant summary

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

The NM_022835.3(PLEKHG2):ā€‹c.166A>Gā€‹(p.Ser56Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000208 in 1,445,544 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

PLEKHG2
NM_022835.3 missense

Scores

2
3
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.38
Variant links:
Genes affected
PLEKHG2 (HGNC:29515): (pleckstrin homology and RhoGEF domain containing G2) The protein encoded by this gene is a RhoGTPase that can activate CDC42 by promoting exchange of GDP for GTP on CDC42. The encoded protein is activated by binding to the beta and gamma subunits of heterotrimeric guanine nucleotide-binding protein. Defects in this gene have been associated with leukodystrophy and acquired microcephaly with or without dystonia. [provided by RefSeq, May 2017]

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=0.1920073).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLEKHG2NM_022835.3 linkc.166A>G p.Ser56Gly missense_variant Exon 3 of 19 ENST00000425673.6 NP_073746.2 Q9H7P9-1
PLEKHG2NM_001351694.2 linkc.166A>G p.Ser56Gly missense_variant Exon 3 of 18 NP_001338623.1
PLEKHG2NM_001351693.2 linkc.110-121A>G intron_variant Intron 2 of 19 NP_001338622.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLEKHG2ENST00000425673.6 linkc.166A>G p.Ser56Gly missense_variant Exon 3 of 19 2 NM_022835.3 ENSP00000392906.2 Q9H7P9-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000208
AC:
3
AN:
1445544
Hom.:
0
Cov.:
31
AF XY:
0.00000279
AC XY:
2
AN XY:
717834
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:
0.00000181
Gnomad4 OTH exome
AF:
0.0000167
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
Mar 06, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.166A>G (p.S56G) alteration is located in exon 3 (coding exon 2) of the PLEKHG2 gene. This alteration results from a A to G substitution at nucleotide position 166, causing the serine (S) at amino acid position 56 to be replaced by a glycine (G). 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
Uncertain
0.42
BayesDel_addAF
Benign
-0.019
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.023
T;.;.;.
Eigen
Benign
0.068
Eigen_PC
Benign
0.045
FATHMM_MKL
Benign
0.27
N
LIST_S2
Benign
0.81
T;T;T;T
M_CAP
Benign
0.077
D
MetaRNN
Benign
0.19
T;T;T;T
MetaSVM
Benign
-0.42
T
MutationAssessor
Uncertain
2.0
M;.;M;.
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-0.57
N;N;N;N
REVEL
Benign
0.13
Sift
Pathogenic
0.0
D;D;D;T
Sift4G
Benign
0.067
T;D;T;D
Polyphen
0.96
P;.;D;.
Vest4
0.47
MutPred
0.18
Loss of phosphorylation at S56 (P = 0.0072);.;Loss of phosphorylation at S56 (P = 0.0072);.;
MVP
0.79
ClinPred
0.96
D
GERP RS
5.0
Varity_R
0.26
gMVP
0.40

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: chr19-39905688; COSMIC: COSV99216719; COSMIC: COSV99216719; API