chr1-98921896-T-C

Variant summary

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

The NM_001037317.2(PLPPR5):ā€‹c.784A>Gā€‹(p.Ile262Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000198 in 1,612,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000033 ( 0 hom., cov: 32)
Exomes š‘“: 0.000018 ( 0 hom. )

Consequence

PLPPR5
NM_001037317.2 missense

Scores

6
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.80
Variant links:
Genes affected
PLPPR5 (HGNC:31703): (phospholipid phosphatase related 5) The protein encoded by this gene is a type 2 member of the phosphatidic acid phosphatase (PAP) family. All type 2 members of this protein family contain 6 transmembrane regions, and a consensus N-glycosylation site. PAPs convert phosphatidic acid to diacylglycerol, and function in de novo synthesis of glycerolipids as well as in receptor-activated signal transduction mediated by phospholipase D. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

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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=0.24925372).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLPPR5NM_001037317.2 linkuse as main transcriptc.784A>G p.Ile262Val missense_variant 4/6 ENST00000263177.5 NP_001032394.1
PLPPR5NM_001010861.3 linkuse as main transcriptc.784A>G p.Ile262Val missense_variant 4/6 NP_001010861.1
PLPPR5XM_011540838.4 linkuse as main transcriptc.736A>G p.Ile246Val missense_variant 5/7 XP_011539140.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLPPR5ENST00000263177.5 linkuse as main transcriptc.784A>G p.Ile262Val missense_variant 4/61 NM_001037317.2 ENSP00000263177 P4Q32ZL2-1
PLPPR5ENST00000370188.7 linkuse as main transcriptc.784A>G p.Ile262Val missense_variant 4/61 ENSP00000359207 A1Q32ZL2-2
PLPPR5ENST00000672681.1 linkuse as main transcriptc.784A>G p.Ile262Val missense_variant 4/7 ENSP00000500930
PLPPR5ENST00000696571.1 linkuse as main transcriptc.619A>G p.Ile207Val missense_variant 5/7 ENSP00000512726

Frequencies

GnomAD3 genomes
AF:
0.0000328
AC:
5
AN:
152214
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000120
AC:
3
AN:
250160
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135244
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000545
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000177
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000185
AC:
27
AN:
1460654
Hom.:
0
Cov.:
30
AF XY:
0.0000151
AC XY:
11
AN XY:
726650
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000225
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000328
AC:
5
AN:
152214
Hom.:
0
Cov.:
32
AF XY:
0.0000403
AC XY:
3
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000565
Hom.:
0
Bravo
AF:
0.0000302
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

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 GeneticsJul 30, 2023The c.784A>G (p.I262V) alteration is located in exon 4 (coding exon 4) of the PLPPR5 gene. This alteration results from a A to G substitution at nucleotide position 784, causing the isoleucine (I) at amino acid position 262 to be replaced by a valine (V). 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
0.094
BayesDel_addAF
Benign
-0.19
T
BayesDel_noAF
Benign
-0.33
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.33
.;T
Eigen
Benign
0.098
Eigen_PC
Uncertain
0.25
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.90
D;D
M_CAP
Benign
0.024
T
MetaRNN
Benign
0.25
T;T
MetaSVM
Benign
-0.79
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.66
T
PROVEAN
Benign
-0.46
N;N
REVEL
Uncertain
0.30
Sift
Benign
0.38
T;T
Sift4G
Benign
0.56
T;T
Polyphen
0.47
P;P
Vest4
0.27
MutPred
0.53
Loss of helix (P = 0.028);Loss of helix (P = 0.028);
MVP
0.068
MPC
0.29
ClinPred
0.58
D
GERP RS
5.5
Varity_R
0.12
gMVP
0.46

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: rs774195359; hg19: chr1-99387452; COSMIC: COSV54171906; API