rs1411674780

Variant names:

• chr19-49851429-C-A
• rs1411674780
• ENST00000391842.6:c.101C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-49851429-C-A
• chr19-49851429-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000391842.6(PTOV1):​c.101C>A​(p.Ser34*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PTOV1 ENST00000391842.6 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

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)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTOV1	NM_001305105.2	c.101C>A	p.Ser34*	stop_gained	Exon 1 of 13		NP_001292034.1
PTOV1	NM_001394010.1	c.101C>A	p.Ser34*	stop_gained	Exon 1 of 12		NP_001380939.1
PTOV1	NM_017432.5	c.101C>A	p.Ser34*	stop_gained	Exon 1 of 13		NP_059128.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTOV1	ENST00000391842.6	c.101C>A	p.Ser34*	stop_gained	Exon 1 of 12	5		ENSP00000375717.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1064480 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 503344

African (AFR) AF: 0.00 AC: 0 AN: 22208

American (AMR) AF: 0.00 AC: 0 AN: 7878

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13488

East Asian (EAS) AF: 0.00 AC: 0 AN: 25248

South Asian (SAS) AF: 0.00 AC: 0 AN: 19648

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2820

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 910212

Other (OTH) AF: 0.00 AC: 0 AN: 42362

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.51	D
BayesDel_noAF	Pathogenic	0.50
CADD	Pathogenic	38
DANN	Uncertain	0.99
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.44
FATHMM_MKL	Uncertain	0.80	D
PhyloP100		1.2
Vest4		0.11
GERP RS		3.5
PromoterAI		-0.065	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.9
Mutation Taster		=55/145	disease causing (fs/PTC)

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

Other links and lift over

dbSNP: rs1411674780; hg19: chr19-50354686;