19-49851350-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000391842.6(PTOV1):​c.22C>T​(p.Pro8Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000513 in 1,098,286 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P8L) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0026 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00019 ( 3 hom. )

Consequence

PTOV1
ENST00000391842.6 missense

Scores

3
1
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.06
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 Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.024394542).
BS2
High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PTOV1NM_001394010.1 linkuse as main transcriptc.22C>T p.Pro8Ser missense_variant 1/12 ENST00000391842.6 NP_001380939.1
PTOV1-AS1NR_040037.1 linkuse as main transcriptn.109+218G>A intron_variant, non_coding_transcript_variant
PTOV1NR_130963.2 linkuse as main transcriptn.251+395C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PTOV1ENST00000391842.6 linkuse as main transcriptc.22C>T p.Pro8Ser missense_variant 1/125 NM_001394010.1 ENSP00000375717 P1Q86YD1-1
PTOV1-AS1ENST00000596521.1 linkuse as main transcriptn.109+218G>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.00256
AC:
380
AN:
148246
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00899
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000535
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:
0.0000451
Gnomad OTH
AF:
0.000982
GnomAD4 exome
AF:
0.000192
AC:
182
AN:
949932
Hom.:
3
Cov.:
32
AF XY:
0.000168
AC XY:
75
AN XY:
446146
show subpopulations
Gnomad4 AFR exome
AF:
0.00861
Gnomad4 AMR exome
AF:
0.000677
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:
0.00000477
Gnomad4 OTH exome
AF:
0.000376
GnomAD4 genome
AF:
0.00257
AC:
381
AN:
148354
Hom.:
1
Cov.:
31
AF XY:
0.00250
AC XY:
181
AN XY:
72394
show subpopulations
Gnomad4 AFR
AF:
0.00898
Gnomad4 AMR
AF:
0.000534
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000451
Gnomad4 OTH
AF:
0.000972
Alfa
AF:
0.00192
Hom.:
0

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 11, 2021The c.22C>T (p.P8S) alteration is located in exon 1 (coding exon 1) of the PTOV1 gene. This alteration results from a C to T substitution at nucleotide position 22, causing the proline (P) at amino acid position 8 to be replaced by a serine (S). 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
Benign
0.21
BayesDel_addAF
Benign
-0.47
T
BayesDel_noAF
Benign
-0.45
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.021
T;T;T
Eigen
Benign
-0.48
Eigen_PC
Benign
-0.36
FATHMM_MKL
Benign
0.40
N
LIST_S2
Benign
0.57
T;.;.
M_CAP
Pathogenic
0.49
D
MetaRNN
Benign
0.024
T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.0
N;N;N
MutationTaster
Benign
1.0
D;N
PrimateAI
Pathogenic
0.91
D
PROVEAN
Benign
-0.60
N;.;.
REVEL
Benign
0.045
Sift
Benign
0.11
T;.;.
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
0.036
B;B;B
Vest4
0.10
MutPred
0.29
Gain of phosphorylation at P8 (P = 0.0019);Gain of phosphorylation at P8 (P = 0.0019);Gain of phosphorylation at P8 (P = 0.0019);
MVP
0.20
MPC
0.44
ClinPred
0.54
D
GERP RS
3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3
Varity_R
0.094
gMVP
0.23

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: rs868811720; hg19: chr19-50354607; API