1-230693314-CAAGT-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePM2
The NM_007357.3(COG2):c.2139_2142del(p.Ser714ThrfsTer2) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A713A) has been classified as Likely benign.
Frequency
Consequence
NM_007357.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG2 | NM_007357.3 | c.2139_2142del | p.Ser714ThrfsTer2 | frameshift_variant | 18/18 | ENST00000366669.9 | |
COG2 | NM_001145036.2 | c.2136_2139del | p.Ser713ThrfsTer2 | frameshift_variant | 18/18 | ||
COG2 | XM_047449445.1 | c.1800_1803del | p.Ser601ThrfsTer2 | frameshift_variant | 16/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG2 | ENST00000366669.9 | c.2139_2142del | p.Ser714ThrfsTer2 | frameshift_variant | 18/18 | 1 | NM_007357.3 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Congenital disorder of glycosylation, type IIq Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2022 | This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser714Thrfs*2) in the COG2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 25 amino acid(s) of the COG2 protein. This variant has not been reported in the literature in individuals affected with COG2-related conditions. 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
Publications
No publications associated with this variant yet.