rs1327694789
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_052874.5(STX1B):c.463A>G(p.Thr155Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000304 in 1,612,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_052874.5 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STX1B | NM_052874.5 | c.463A>G | p.Thr155Ala | missense_variant, splice_region_variant | 6/10 | ENST00000215095.11 | |
STX1B | XM_017022893.2 | c.445A>G | p.Thr149Ala | missense_variant, splice_region_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STX1B | ENST00000215095.11 | c.463A>G | p.Thr155Ala | missense_variant, splice_region_variant | 6/10 | 1 | NM_052874.5 | P1 | |
STX1B | ENST00000565419.2 | c.463A>G | p.Thr155Ala | missense_variant, splice_region_variant | 6/9 | 2 | |||
STX1B | ENST00000566211.1 | n.94A>G | splice_region_variant, non_coding_transcript_exon_variant | 1/2 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152078Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249344Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135016
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1460450Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 726468
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152078Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74294
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 15, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Generalized epilepsy with febrile seizures plus, type 9 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 10, 2023 | This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 155 of the STX1B protein (p.Thr155Ala). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with STX1B-related conditions. ClinVar contains an entry for this variant (Variation ID: 542094). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at