dbSNP rs1185809399: PLPPR3:p.Glu699Lys (chr19-812632-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001270366.2(PLPPR3):c.2095G>A(p.Glu699Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 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. E699V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PLPPR3
NM_001270366.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.67

Publications

0 publications found

Variant links:

Genes affected

PLPPR3 (HGNC:23497): (phospholipid phosphatase related 3) The proteins in the lipid phosphate phosphatase (LPP) family, including PRG2, are integral membrane proteins that modulate bioactive lipid phosphates including phosphatidate, lysophosphatidate, and sphingosine-1-phosphate in the context of cell migration, neurite retraction, and mitogenesis (Brauer et al., 2003 [PubMed 12730698]).[supplied by OMIM, Mar 2008]

PLPPR3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.10937804).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001270366.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPPR3	NM_001270366.2	MANE Select	c.2095G>A	p.Glu699Lys	missense	Exon 8 of 8	NP_001257295.1	Q6T4P5-1
	PLPPR3	NM_024888.3		c.2179G>A	p.Glu727Lys	missense	Exon 7 of 7	NP_079164.1	Q6T4P5-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PLPPR3	ENST00000520876.8	TSL:1 MANE Select	c.2095G>A	p.Glu699Lys	missense	Exon 8 of 8	ENSP00000430297.1	Q6T4P5-1
PLPPR3	ENST00000359894.6	TSL:1	c.2179G>A	p.Glu727Lys	missense	Exon 7 of 7	ENSP00000352962.2	Q6T4P5-3
PLPPR3	ENST00000947290.1		c.2179G>A	p.Glu727Lys	missense	Exon 6 of 6	ENSP00000617349.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

961436

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

463536

African (AFR)

AF:

0.00

AC:

AN:

17286

American (AMR)

AF:

0.00

AC:

AN:

6252

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

9166

East Asian (EAS)

AF:

0.00

AC:

AN:

7604

South Asian (SAS)

AF:

0.00

AC:

AN:

41124

European-Finnish (FIN)

AF:

0.00

AC:

AN:

11520

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2094

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

833446

Other (OTH)

AF:

0.00

AC:

AN:

32944

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.23

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.023

Eigen

Benign

-0.54

Eigen_PC

Benign

-0.52

FATHMM_MKL

Benign

0.067

LIST_S2

Benign

0.53

M_CAP

Benign

0.039

MetaRNN

Benign

0.11

MetaSVM

Benign

-1.0

PhyloP100

3.7

PrimateAI

Pathogenic

0.80

PROVEAN

Benign

-1.4

REVEL

Benign

0.086

Sift

Benign

0.11

Sift4G

Benign

0.36

Polyphen

0.82

Vest4

0.18

MutPred

0.32

Gain of loop (P = 3e-04)

MVP

0.31

MPC

0.46

ClinPred

0.55

GERP RS

4.2

Varity_R

0.20

gMVP

0.22

Mutation Taster

=83/17

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over