1-98956630-G-A

Variant summary

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

The NM_001037317.2(PLPPR5):​c.349C>T​(p.Arg117Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000221 in 1,586,096 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00023 ( 0 hom. )

Consequence

PLPPR5
NM_001037317.2 missense

Scores

8
6
4

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.85
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLPPR5NM_001037317.2 linkuse as main transcriptc.349C>T p.Arg117Cys missense_variant 2/6 ENST00000263177.5 NP_001032394.1
PLPPR5NM_001010861.3 linkuse as main transcriptc.349C>T p.Arg117Cys missense_variant 2/6 NP_001010861.1
PLPPR5XM_011540838.4 linkuse as main transcriptc.301C>T p.Arg101Cys missense_variant 3/7 XP_011539140.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLPPR5ENST00000263177.5 linkuse as main transcriptc.349C>T p.Arg117Cys missense_variant 2/61 NM_001037317.2 ENSP00000263177 P4Q32ZL2-1
PLPPR5ENST00000370188.7 linkuse as main transcriptc.349C>T p.Arg117Cys missense_variant 2/61 ENSP00000359207 A1Q32ZL2-2
PLPPR5ENST00000672681.1 linkuse as main transcriptc.349C>T p.Arg117Cys missense_variant 2/7 ENSP00000500930
PLPPR5ENST00000696571.1 linkuse as main transcriptc.184C>T p.Arg62Cys missense_variant 3/7 ENSP00000512726

Frequencies

GnomAD3 genomes
AF:
0.000112
AC:
17
AN:
152100
Hom.:
0
Cov.:
31
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:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000283
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000191
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000177
AC:
40
AN:
225916
Hom.:
0
AF XY:
0.000163
AC XY:
20
AN XY:
122946
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000372
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000379
Gnomad FIN exome
AF:
0.000567
Gnomad NFE exome
AF:
0.000236
Gnomad OTH exome
AF:
0.000186
GnomAD4 exome
AF:
0.000233
AC:
334
AN:
1433878
Hom.:
0
Cov.:
30
AF XY:
0.000232
AC XY:
165
AN XY:
712700
show subpopulations
Gnomad4 AFR exome
AF:
0.0000631
Gnomad4 AMR exome
AF:
0.0000527
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000250
Gnomad4 FIN exome
AF:
0.000472
Gnomad4 NFE exome
AF:
0.000267
Gnomad4 OTH exome
AF:
0.000152
GnomAD4 genome
AF:
0.000112
AC:
17
AN:
152218
Hom.:
0
Cov.:
31
AF XY:
0.000121
AC XY:
9
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000283
Gnomad4 NFE
AF:
0.000191
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000248
Hom.:
0
Bravo
AF:
0.0000680
ExAC
AF:
0.000132
AC:
16

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 GeneticsOct 20, 2023The c.349C>T (p.R117C) alteration is located in exon 2 (coding exon 2) of the PLPPR5 gene. This alteration results from a C to T substitution at nucleotide position 349, causing the arginine (R) at amino acid position 117 to be replaced by a cysteine (C). 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
Pathogenic
0.84
BayesDel_addAF
Uncertain
0.048
T
BayesDel_noAF
Pathogenic
0.15
CADD
Pathogenic
31
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.24
.;T
Eigen
Uncertain
0.61
Eigen_PC
Uncertain
0.53
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Pathogenic
0.99
D;D
M_CAP
Benign
0.084
D
MetaRNN
Uncertain
0.70
D;D
MetaSVM
Benign
-0.50
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.85
D
PROVEAN
Pathogenic
-6.9
D;D
REVEL
Uncertain
0.47
Sift
Pathogenic
0.0
D;D
Sift4G
Pathogenic
0.0010
D;D
Polyphen
1.0
D;D
Vest4
0.89
MVP
0.42
MPC
1.8
ClinPred
0.70
D
GERP RS
3.8
Varity_R
0.74
gMVP
0.92

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: rs200017242; hg19: chr1-99422186; COSMIC: COSV54170322; API