chr1-98914823-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001037317.2(PLPPR5):c.896G>A(p.Arg299Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,612,996 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
PLPPR5
NM_001037317.2 missense
NM_001037317.2 missense
Scores
8
10
Clinical Significance
Conservation
PhyloP100: 6.75
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 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 |
---|---|---|---|---|---|---|---|---|
PLPPR5 | NM_001037317.2 | c.896G>A | p.Arg299Gln | missense_variant | 5/6 | ENST00000263177.5 | NP_001032394.1 | |
PLPPR5 | NM_001010861.3 | c.896G>A | p.Arg299Gln | missense_variant | 5/6 | NP_001010861.1 | ||
PLPPR5 | XM_011540838.4 | c.848G>A | p.Arg283Gln | missense_variant | 6/7 | XP_011539140.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPPR5 | ENST00000263177.5 | c.896G>A | p.Arg299Gln | missense_variant | 5/6 | 1 | NM_001037317.2 | ENSP00000263177 | P4 | |
PLPPR5 | ENST00000370188.7 | c.896G>A | p.Arg299Gln | missense_variant | 5/6 | 1 | ENSP00000359207 | A1 | ||
PLPPR5 | ENST00000672681.1 | c.896G>A | p.Arg299Gln | missense_variant | 5/7 | ENSP00000500930 | ||||
PLPPR5 | ENST00000696571.1 | c.731G>A | p.Arg244Gln | missense_variant | 6/7 | ENSP00000512726 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250658Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135512
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GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460978Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726822
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GnomAD4 genome AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74252
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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 submitter | clinical testing | Ambry Genetics | Apr 19, 2024 | The c.896G>A (p.R299Q) alteration is located in exon 5 (coding exon 5) of the PLPPR5 gene. This alteration results from a G to A substitution at nucleotide position 896, causing the arginine (R) at amino acid position 299 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;D
Sift4G
Uncertain
D;D
Polyphen
P;P
Vest4
MutPred
Loss of phosphorylation at S302 (P = 0.0602);Loss of phosphorylation at S302 (P = 0.0602);
MVP
MPC
0.16
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at