chr19-39415019-C-A

Variant summary

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

The NM_022835.3(PLEKHG2):​c.137C>A​(p.Pro46His) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PLEKHG2
NM_022835.3 missense

Scores

5
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.57
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]

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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=0.20852154).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLEKHG2NM_022835.3 linkc.137C>A p.Pro46His missense_variant Exon 3 of 19 ENST00000425673.6 NP_073746.2 Q9H7P9-1
PLEKHG2NM_001351694.2 linkc.137C>A p.Pro46His missense_variant Exon 3 of 18 NP_001338623.1
PLEKHG2NM_001351693.2 linkc.110-150C>A 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.137C>A p.Pro46His missense_variant Exon 3 of 19 2 NM_022835.3 ENSP00000392906.2 Q9H7P9-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1445836
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
717182
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:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000660
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.044
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.0061
T;.;.;.
Eigen
Benign
-0.054
Eigen_PC
Benign
-0.12
FATHMM_MKL
Benign
0.55
D
LIST_S2
Benign
0.75
T;T;T;T
M_CAP
Uncertain
0.20
D
MetaRNN
Benign
0.21
T;T;T;T
MetaSVM
Benign
-0.63
T
MutationAssessor
Benign
1.7
L;.;L;.
PrimateAI
Uncertain
0.75
T
PROVEAN
Benign
-2.2
N;D;N;N
REVEL
Benign
0.13
Sift
Uncertain
0.012
D;D;D;D
Sift4G
Uncertain
0.0020
D;D;D;D
Polyphen
0.99
D;.;D;.
Vest4
0.32
MutPred
0.20
Loss of glycosylation at P46 (P = 0.0471);.;Loss of glycosylation at P46 (P = 0.0471);.;
MVP
0.72
ClinPred
0.94
D
GERP RS
3.9
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.11
gMVP
0.25

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: rs1211640713; hg19: chr19-39905659; API