rs1379794257

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_017432.5(PTOV1):​c.65G>A​(p.Arg22His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000017 in 1,174,120 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.0000068 ( 0 hom., cov: 32)
Exomes 𝑓: 9.7e-7 ( 0 hom. )

Consequence

PTOV1
NM_017432.5 missense

Scores

2
2
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.97
Variant links:
Genes affected
PTOV1 (HGNC:9632): (PTOV1 extended AT-hook containing adaptor protein) This gene encodes a protein that was found to be overexpressed in prostate adenocarcinomas. The encoded protein was found to interact with the lipid raft protein flotillin-1 and shuttle it from the cytoplasm to the nucleus in a cell cycle dependent manner. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]
PTOV1-AS1 (HGNC:44174): (PTOV1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3907362).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTOV1NM_001305105.2 linkc.65G>A p.Arg22His missense_variant Exon 1 of 13 NP_001292034.1 Q86YD1-1
PTOV1NM_001394010.1 linkc.65G>A p.Arg22His missense_variant Exon 1 of 12 NP_001380939.1
PTOV1NM_017432.5 linkc.65G>A p.Arg22His missense_variant Exon 1 of 13 NP_059128.2 Q86YD1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTOV1ENST00000391842.6 linkc.65G>A p.Arg22His missense_variant Exon 1 of 12 5 ENSP00000375717.1 Q86YD1-1

Frequencies

GnomAD3 genomes
AF:
0.00000676
AC:
1
AN:
147906
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00325
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
9.75e-7
AC:
1
AN:
1026120
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
483920
show subpopulations
Gnomad4 AFR exome
AF:
0.0000478
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
AF:
0.00000676
AC:
1
AN:
148000
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
72184
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.23
BayesDel_addAF
Benign
-0.075
T
BayesDel_noAF
Benign
-0.35
CADD
Uncertain
25
DANN
Uncertain
0.99
DEOGEN2
Benign
0.019
T;T;T
Eigen
Benign
0.091
Eigen_PC
Benign
0.050
FATHMM_MKL
Benign
0.52
D
LIST_S2
Benign
0.68
T;.;.
M_CAP
Pathogenic
0.71
D
MetaRNN
Benign
0.39
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;N
PrimateAI
Pathogenic
0.92
D
PROVEAN
Benign
-0.22
N;.;.
REVEL
Benign
0.27
Sift
Uncertain
0.015
D;.;.
Sift4G
Benign
0.15
T;T;T
Polyphen
0.99
D;D;D
Vest4
0.25
MutPred
0.26
Loss of methylation at R22 (P = 0.0109);Loss of methylation at R22 (P = 0.0109);Loss of methylation at R22 (P = 0.0109);
MVP
0.31
MPC
0.48
ClinPred
0.85
D
GERP RS
3.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.6
Varity_R
0.10
gMVP
0.29

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: rs1379794257; hg19: chr19-50354650; API