GeneBe

rs4767884

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000458477.6(PXN):​c.-183A>T variant causes a 5 prime UTR premature start codon gain 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: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

PXN
ENST00000458477.6 5_prime_UTR_premature_start_codon_gain

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0780

Publications

42 publications found
Variant links:
Genes affected
PXN (HGNC:9718): (paxillin) This gene encodes a cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion). Alternatively spliced transcript variants encoding different isoforms have been described for this gene. These isoforms exhibit different expression pattern, and have different biochemical, as well as physiological properties (PMID:9054445). [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09579864).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PXNNM_001385981.1 linkc.217A>T p.Ser73Cys missense_variant Exon 2 of 15 ENST00000637617.2 NP_001372910.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PXNENST00000637617.2 linkc.217A>T p.Ser73Cys missense_variant Exon 2 of 15 5 NM_001385981.1 ENSP00000489840.1 A0A1B0GTU4

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1441978
Hom.:
0
Cov.:
50
AF XY:
0.00
AC XY:
0
AN XY:
715490
African (AFR)
AF:
0.00
AC:
0
AN:
33210
American (AMR)
AF:
0.00
AC:
0
AN:
41212
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25470
East Asian (EAS)
AF:
0.00
AC:
0
AN:
38950
South Asian (SAS)
AF:
0.00
AC:
0
AN:
84072
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51726
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5664
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1102024
Other (OTH)
AF:
0.00
AC:
0
AN:
59650
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.063
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
13
DANN
Benign
0.93
DEOGEN2
Benign
0.21
.;T;.;T;T;.
Eigen
Benign
-0.91
Eigen_PC
Benign
-0.99
FATHMM_MKL
Benign
0.23
N
LIST_S2
Benign
0.66
T;T;T;T;T;T
M_CAP
Benign
0.058
D
MetaRNN
Benign
0.096
T;T;T;T;T;T
MetaSVM
Benign
-0.91
T
MutationAssessor
Benign
1.1
L;L;L;.;.;.
PhyloP100
-0.078
PrimateAI
Benign
0.24
T
PROVEAN
Benign
-0.78
N;N;N;N;.;N
REVEL
Benign
0.061
Sift
Benign
0.032
D;D;T;T;.;D
Sift4G
Benign
0.19
T;T;T;T;.;.
Polyphen
0.71, 0.41
.;P;B;.;.;.
Vest4
0.27
MutPred
0.33
Loss of phosphorylation at S73 (P = 0.0485);Loss of phosphorylation at S73 (P = 0.0485);Loss of phosphorylation at S73 (P = 0.0485);.;Loss of phosphorylation at S73 (P = 0.0485);.;
MVP
0.56
MPC
0.17
ClinPred
0.13
T
GERP RS
0.22
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.054
gMVP
0.18
Mutation Taster
=300/0
polymorphism

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

Other links and lift over

dbSNP: rs4767884; hg19: chr12-120661977; API