7-82758711-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_033026.6(PCLO):āc.15293T>Cā(p.Leu5098Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000701 in 1,425,942 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 7.0e-7 ( 0 hom. )
Consequence
PCLO
NM_033026.6 missense
NM_033026.6 missense
Scores
2
7
8
Clinical Significance
Conservation
PhyloP100: 7.50
Genes affected
PCLO (HGNC:13406): (piccolo presynaptic cytomatrix protein) The protein encoded by this gene is part of the presynaptic cytoskeletal matrix, which is involved in establishing active synaptic zones and in synaptic vesicle trafficking. Variations in this gene have been associated with bipolar disorder and major depressive disorder. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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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 |
---|---|---|---|---|---|---|---|---|
PCLO | NM_033026.6 | c.15293T>C | p.Leu5098Ser | missense_variant | 25/25 | ENST00000333891.14 | NP_149015.2 | |
PCLO | XM_047420210.1 | c.15476T>C | p.Leu5159Ser | missense_variant | 26/26 | XP_047276166.1 | ||
PCLO | XM_047420211.1 | c.15002T>C | p.Leu5001Ser | missense_variant | 26/26 | XP_047276167.1 | ||
PCLO | XM_017012006.3 | c.8381T>C | p.Leu2794Ser | missense_variant | 24/24 | XP_016867495.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PCLO | ENST00000333891.14 | c.15293T>C | p.Leu5098Ser | missense_variant | 25/25 | 2 | NM_033026.6 | ENSP00000334319.8 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1425942Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 711416
GnomAD4 exome
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1
AN:
1425942
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25
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0
AN XY:
711416
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 06, 2023 | The c.15293T>C (p.L5098S) alteration is located in exon 25 (coding exon 25) of the PCLO gene. This alteration results from a T to C substitution at nucleotide position 15293, causing the leucine (L) at amino acid position 5098 to be replaced by a serine (S). 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
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
PrimateAI
Pathogenic
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Uncertain
D
Sift4G
Uncertain
D
Vest4
MutPred
Loss of stability (P = 0.0098);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at