chr1-99004658-G-A

Variant summary

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

The NM_001037317.2(PLPPR5):​c.14C>T​(p.Pro5Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,610,524 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 (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000036 ( 0 hom. )

Consequence

PLPPR5
NM_001037317.2 missense

Scores

3
3
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.30
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]
PLPPR5-AS1 (HGNC:55720): (PLPPR5 antisense RNA 1)

Genome browser will be placed here

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=0.07566923).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLPPR5NM_001037317.2 linkuse as main transcriptc.14C>T p.Pro5Leu missense_variant 1/6 ENST00000263177.5 NP_001032394.1
PLPPR5-AS1NR_033940.1 linkuse as main transcriptn.370+13G>A intron_variant, non_coding_transcript_variant
PLPPR5NM_001010861.3 linkuse as main transcriptc.14C>T p.Pro5Leu missense_variant 1/6 NP_001010861.1
PLPPR5XM_011540838.4 linkuse as main transcriptc.1-35C>T intron_variant XP_011539140.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLPPR5ENST00000263177.5 linkuse as main transcriptc.14C>T p.Pro5Leu missense_variant 1/61 NM_001037317.2 ENSP00000263177 P4Q32ZL2-1
PLPPR5-AS1ENST00000658279.1 linkuse as main transcriptn.202+13G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
152008
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000864
AC:
21
AN:
243148
Hom.:
0
AF XY:
0.000128
AC XY:
17
AN XY:
132774
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000591
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000563
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000923
Gnomad OTH exome
AF:
0.000168
GnomAD4 exome
AF:
0.0000363
AC:
53
AN:
1458516
Hom.:
0
Cov.:
31
AF XY:
0.0000593
AC XY:
43
AN XY:
725576
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000449
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000547
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000664
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
152008
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000329
Hom.:
0
Bravo
AF:
0.0000151
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000826
AC:
10

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 06, 2021The c.14C>T (p.P5L) alteration is located in exon 1 (coding exon 1) of the PLPPR5 gene. This alteration results from a C to T substitution at nucleotide position 14, causing the proline (P) at amino acid position 5 to be replaced by a leucine (L). 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
0.27
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.53
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.064
.;T
Eigen
Benign
-0.31
Eigen_PC
Benign
-0.21
FATHMM_MKL
Benign
0.53
D
LIST_S2
Benign
0.71
T;T
M_CAP
Pathogenic
0.41
D
MetaRNN
Benign
0.076
T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
1.0
D;D
PrimateAI
Pathogenic
0.81
D
PROVEAN
Uncertain
-3.0
D;D
REVEL
Benign
0.098
Sift
Pathogenic
0.0
D;D
Sift4G
Uncertain
0.013
D;D
Polyphen
0.0
B;B
Vest4
0.13
MVP
0.043
MPC
0.59
ClinPred
0.19
T
GERP RS
2.4
Varity_R
0.28
gMVP
0.78

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: rs142171434; hg19: chr1-99470214; API