rs761948281
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001003787.4(STRADA):c.905C>A(p.Thr302Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000191 in 1,567,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T302T) has been classified as Likely benign.
Frequency
Consequence
NM_001003787.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STRADA | NM_001003787.4 | c.905C>A | p.Thr302Asn | missense_variant | 11/13 | ENST00000336174.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STRADA | ENST00000336174.12 | c.905C>A | p.Thr302Asn | missense_variant | 11/13 | 1 | NM_001003787.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000678 AC: 1AN: 147464Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232518Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 124564
GnomAD4 exome AF: 0.00000141 AC: 2AN: 1420392Hom.: 0 Cov.: 44 AF XY: 0.00000142 AC XY: 1AN XY: 703838
GnomAD4 genome ? AF: 0.00000678 AC: 1AN: 147464Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 71418
ClinVar
Submissions by phenotype
Polyhydramnios, megalencephaly, and symptomatic epilepsy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 30, 2018 | This sequence change replaces threonine with asparagine at codon 302 of the STRADA protein (p.Thr302Asn). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and asparagine. This variant is present in population databases (rs761948281, ExAC 0.01%). 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with STRADA-related disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at