rs483352901
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_StrongPP5_Moderate
The NM_003764.4(STX11):c.369_376delinsTGG(p.Val124GlyfsTer60) variant causes a frameshift change. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A123A) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Consequence
STX11
NM_003764.4 frameshift
NM_003764.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.58
Genes affected
STX11 (HGNC:11429): (syntaxin 11) This gene encodes a member of the syntaxin family. Syntaxins have been implicated in the targeting and fusion of intracellular transport vesicles. This family member may regulate protein transport among late endosomes and the trans-Golgi network. Mutations in this gene have been associated with familial hemophagocytic lymphohistiocytosis. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 13 pathogenic variants in the truncated region.
PP5
?
Variant 6-144186996-AGTGGCGC-TGG is Pathogenic according to our data. Variant chr6-144186996-AGTGGCGC-TGG is described in ClinVar as [Pathogenic]. Clinvar id is 5263.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX11 | NM_003764.4 | c.369_376delinsTGG | p.Val124GlyfsTer60 | frameshift_variant | 2/2 | ENST00000367568.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX11 | ENST00000367568.5 | c.369_376delinsTGG | p.Val124GlyfsTer60 | frameshift_variant | 2/2 | 1 | NM_003764.4 | P1 | |
STX11 | ENST00000698355.1 | c.369_376delinsTGG | p.Val124GlyfsTer60 | frameshift_variant | 3/3 | P1 | |||
STX11 | ENST00000698356.1 | c.369_376delinsTGG | p.Val124GlyfsTer60 | frameshift_variant | 4/4 | P1 | |||
STX11 | ENST00000698357.1 | c.369_376delinsTGG | p.Val124GlyfsTer60 | frameshift_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 15, 2005 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Oct 02, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at