12-14511699-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_024829.6(PLBD1):āc.857C>Gā(p.Ser286Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 1,613,884 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00013 ( 0 hom., cov: 32)
Exomes š: 0.00010 ( 1 hom. )
Consequence
PLBD1
NM_024829.6 missense
NM_024829.6 missense
Scores
11
5
3
Clinical Significance
Conservation
PhyloP100: 9.27
Genes affected
PLBD1 (HGNC:26215): (phospholipase B domain containing 1) Predicted to enable phospholipase activity. Predicted to be involved in phospholipid catabolic process. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.848
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLBD1 | NM_024829.6 | c.857C>G | p.Ser286Cys | missense_variant | 7/11 | ENST00000240617.10 | NP_079105.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLBD1 | ENST00000240617.10 | c.857C>G | p.Ser286Cys | missense_variant | 7/11 | 1 | NM_024829.6 | ENSP00000240617 | P1 | |
PLBD1 | ENST00000541800.6 | n.480C>G | non_coding_transcript_exon_variant | 2/3 | 3 | |||||
PLBD1 | ENST00000541618.1 | c.*514C>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/6 | 5 | ENSP00000441278 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152108Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000147 AC: 37AN: 251088Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135774
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GnomAD4 exome AF: 0.000105 AC: 153AN: 1461776Hom.: 1 Cov.: 34 AF XY: 0.000110 AC XY: 80AN XY: 727200
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74290
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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 | Dec 08, 2023 | The c.857C>G (p.S286C) alteration is located in exon 7 (coding exon 7) of the PLBD1 gene. This alteration results from a C to G substitution at nucleotide position 857, causing the serine (S) at amino acid position 286 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Pathogenic
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
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