rs2074236321

Variant summary

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

The NM_017432.5(PTOV1):​c.16C>A​(p.Arg6Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,088,998 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: 31)
Exomes 𝑓: 0.000021 ( 0 hom. )

Consequence

PTOV1
NM_017432.5 missense

Scores

4
2
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.668
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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2067101).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTOV1NM_001305105.2 linkc.16C>A p.Arg6Ser missense_variant Exon 1 of 13 NP_001292034.1 Q86YD1-1
PTOV1NM_001394010.1 linkc.16C>A p.Arg6Ser missense_variant Exon 1 of 12 NP_001380939.1
PTOV1NM_017432.5 linkc.16C>A p.Arg6Ser 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.16C>A p.Arg6Ser missense_variant Exon 1 of 12 5 ENSP00000375717.1 Q86YD1-1

Frequencies

GnomAD3 genomes
AF:
0.00000676
AC:
1
AN:
147986
Hom.:
0
Cov.:
31
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:
0.00
Gnomad NFE
AF:
0.0000151
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000213
AC:
20
AN:
941012
Hom.:
0
Cov.:
32
AF XY:
0.0000226
AC XY:
10
AN XY:
441610
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:
0.0000240
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000676
AC:
1
AN:
147986
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
72118
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:
0.0000151
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.77
BayesDel_addAF
Uncertain
0.018
T
BayesDel_noAF
Benign
-0.21
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Benign
0.017
T;T;T
Eigen
Benign
-0.045
Eigen_PC
Benign
-0.051
FATHMM_MKL
Benign
0.59
D
LIST_S2
Benign
0.54
T;.;.
M_CAP
Pathogenic
0.56
D
MetaRNN
Benign
0.21
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;N
PrimateAI
Pathogenic
0.94
D
PROVEAN
Benign
-0.080
N;.;.
REVEL
Benign
0.15
Sift
Pathogenic
0.0
D;.;.
Sift4G
Benign
0.15
T;T;T
Polyphen
0.96
D;D;D
Vest4
0.27
MutPred
0.22
Gain of phosphorylation at R6 (P = 0.0042);Gain of phosphorylation at R6 (P = 0.0042);Gain of phosphorylation at R6 (P = 0.0042);
MVP
0.37
MPC
0.39
ClinPred
0.62
D
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.9
Varity_R
0.33
gMVP
0.39

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: rs2074236321; hg19: chr19-50354601; API