rs1555907463
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_203446.3(SYNJ1):c.395G>A(p.Trp132*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
SYNJ1
NM_203446.3 stop_gained
NM_203446.3 stop_gained
Scores
5
1
1
Clinical Significance
Conservation
PhyloP100: 7.46
Genes affected
SYNJ1 (HGNC:11503): (synaptojanin 1) This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 21-32699922-C-T is Pathogenic according to our data. Variant chr21-32699922-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 549503.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early-onset Parkinson disease 20 Pathogenic:1
Pathogenic, criteria provided, single submitter | case-control | Institute for Human Genetics, University Medical Center Freiburg | Aug 30, 2016 | This variant was found in two German patients with epilepsy early in the disease course, followed by progressive generalized dopa-responsive dystonia associated with severe action tremor of the tongue, head, and extremities in their early teen years, and cognitive deterioration. We identified compound heterozygous mutations (NP_982271.2:p.Trp171*/NP_982271.2:p.Arg258Gln) in the SYNJ1 gene, affecting the N-terminal suppressor of actin1 (SAC1)-like domain of the SYNJ1 protein. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
Vest4
GERP RS
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