rs553120567
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_006279.5(ST3GAL3):c.1079G>A(p.Arg360Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000349 in 1,614,142 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R360W) has been classified as Uncertain significance.
Frequency
Consequence
NM_006279.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ST3GAL3 | NM_006279.5 | c.1079G>A | p.Arg360Gln | missense_variant | 12/12 | ENST00000347631.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ST3GAL3 | ENST00000347631.8 | c.1079G>A | p.Arg360Gln | missense_variant | 12/12 | 5 | NM_006279.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000460 AC: 70AN: 152234Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000728 AC: 183AN: 251432Hom.: 0 AF XY: 0.000912 AC XY: 124AN XY: 135896
GnomAD4 exome AF: 0.000338 AC: 494AN: 1461790Hom.: 2 Cov.: 32 AF XY: 0.000469 AC XY: 341AN XY: 727204
GnomAD4 genome ? AF: 0.000453 AC: 69AN: 152352Hom.: 1 Cov.: 33 AF XY: 0.000510 AC XY: 38AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 18, 2014 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2022 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 10, 2017 | The p.R360Q variant (also known as c.1079G>A), located in coding exon 11 of the ST3GAL3 gene, results from a G to A substitution at nucleotide position 1079. The arginine at codon 360 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Intellectual disability, autosomal recessive 12;C3554316:Developmental and epileptic encephalopathy, 15 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | ST3GAL3 NM_174963.4 exon 13 p.Arg429Gln (c.1286G>A): This variant has not been reported in the literature but is present in 0.4% (135/30616) of South Asian alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/variant/1-44395844-G-A). This variant is present in ClinVar (Variation ID:130377). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
ST3GAL3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 06, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Early infantile epileptic encephalopathy with suppression bursts Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at