rs202190749

Variant names:

• chr19-49854722-A-C
• rs202190749
• ENST00000391842.6:c.380A>C

Your query was ambiguous. Multiple possible variants found:

• chr19-49854722-A-C
• chr19-49854722-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001364747.2(PTOV1):​c.425A>C​(p.Gln142Pro) variant causes a missense 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. 14/21 in silico tools predict 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: 32)
• Consequence: PTOV1 NM_001364747.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

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]

ENSG00000268047 (HGNC:):

ACMG classification

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=0.07497129).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTOV1	NM_001364747.2	c.425A>C	p.Gln142Pro	missense_variant	Exon 3 of 13		NP_001351676.1
PTOV1	NM_001364749.2	c.425A>C	p.Gln142Pro	missense_variant	Exon 3 of 13		NP_001351678.1
PTOV1	NM_001305105.2	c.380A>C	p.Gln127Pro	missense_variant	Exon 3 of 13		NP_001292034.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTOV1	ENST00000391842.6	c.380A>C	p.Gln127Pro	missense_variant	Exon 3 of 12	5		ENSP00000375717.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.088
BayesDel_addAF	Benign	-0.046	T
BayesDel_noAF	Benign	-0.30
CADD	Benign	18
DANN	Benign	0.90
DEOGEN2	Benign	0.014	T;.;.;T;T;T;T
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.49
FATHMM_MKL	Benign	0.39	N
LIST_S2	Benign	0.79	T;T;T;T;.;.;T
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.075	T;T;T;T;T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.3	.;.;.;L;L;L;.
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-2.0	.;.;.;N;.;.;.
REVEL	Benign	0.034
Sift	Benign	0.42	.;.;.;T;.;.;.
Sift4G	Benign	0.27	T;T;T;T;T;T;T
Polyphen		0.0	.;.;.;B;B;B;.
Vest4		0.37, 0.36, 0.32, 0.32, 0.32
MutPred		0.34		.;.;.;Loss of sheet (P = 0.0457);Loss of sheet (P = 0.0457);Loss of sheet (P = 0.0457);.;
MVP		0.48
MPC		0.13
ClinPred		0.093	T
GERP RS		-0.21
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.23
gMVP		0.87

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

Other links and lift over

dbSNP: rs202190749; hg19: chr19-50357979;