rs1294224206
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM1PM2BP4_Moderate
The NM_006950.3(SYN1):c.184T>G(p.Ser62Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000009 in 111,139 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006950.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYN1 | NM_006950.3 | c.184T>G | p.Ser62Ala | missense_variant | 1/13 | ENST00000295987.13 | NP_008881.2 | |
SYN1 | NM_133499.2 | c.184T>G | p.Ser62Ala | missense_variant | 1/13 | NP_598006.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYN1 | ENST00000295987.13 | c.184T>G | p.Ser62Ala | missense_variant | 1/13 | 2 | NM_006950.3 | ENSP00000295987 | P3 | |
SYN1 | ENST00000340666.5 | c.184T>G | p.Ser62Ala | missense_variant | 1/13 | 1 | ENSP00000343206 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111139Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33433
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111139Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33433
ClinVar
Submissions by phenotype
Epilepsy, X-linked 1, with variable learning disabilities and behavior disorders Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 11, 2023 | This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 62 of the SYN1 protein (p.Ser62Ala). 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. 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. ClinVar contains an entry for this variant (Variation ID: 465094). This variant has not been reported in the literature in individuals affected with SYN1-related conditions. This variant is not present in population databases (gnomAD no frequency). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at