3-15458197-G-A
Variant summary
Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_005677.4(COLQ):c.943C>T(p.Arg315*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,613,612 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_005677.4 stop_gained
Scores
Clinical Significance
Conservation
Publications
- congenital myasthenic syndrome 5Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, PanelApp Australia
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ACMG classification
Our verdict: Pathogenic. The variant received 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COLQ | NM_005677.4 | c.943C>T | p.Arg315* | stop_gained | Exon 13 of 17 | ENST00000383788.10 | NP_005668.2 | |
COLQ | NM_080538.2 | c.913C>T | p.Arg305* | stop_gained | Exon 13 of 17 | NP_536799.1 | ||
COLQ | NM_080539.4 | c.841C>T | p.Arg281* | stop_gained | Exon 12 of 16 | NP_536800.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COLQ | ENST00000383788.10 | c.943C>T | p.Arg315* | stop_gained | Exon 13 of 17 | 1 | NM_005677.4 | ENSP00000373298.3 | ||
COLQ | ENST00000603808.5 | c.943C>T | p.Arg315* | stop_gained | Exon 13 of 17 | 1 | ENSP00000474271.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000159 AC: 4AN: 251456 AF XY: 0.0000147 show subpopulations
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461478Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727044 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74310 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 5 Pathogenic:5
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A homozygous nonsense variant, NM_005677.3(COLQ):c.943C>T, has been identified in exon 13 of 17 of the COLQ gene. The variant is predicted to result in a premature stop codon at position 315 of the protein, NP_005668.2(COLQ):p.(Arg315*). This variant is predicted to result in loss of protein function either through truncation (including the C-terminal end region) or nonsense-mediated decay, which is a reported mechanism of pathogenicity for this gene. The variant is present in the gnomAD database at a frequency of 0.0016% (4 heterozygotes, 0 homozygotes). The variant has been previously described as pathogenic and segregated with disease in three affected members of a family (ClinVar, Ohno et al., (1999)). Additionally, functional analysis of the congenital end-pate acetylcholinesterase (AChE) showed reduced expression preventing the anchoring of the AChE to the synaptic basal lamina (Ohno et al., (1999)). Based on the information available at the time of curation, this variant has been classified as PATHOGENIC. -
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This variant is present in population databases (rs121908924, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Arg315*) in the COLQ gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COLQ are known to be pathogenic (PMID: 22678886). This premature translational stop signal has been observed in individuals with congenital myasthenic syndrome (PMID: 10441569). It has also been observed to segregate with disease in related individuals. For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 6655). -
not provided Pathogenic:2
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Published functional studies demonstrate a damaging effect, as the variant caused the failure of forming the expected AChE complexes (PMID: 10441569); Observed with another variant in the COLQ gene in a patient with AChE deficiency in published literature; however, it is unclear whether the variants were on the same (in cis) or on opposite alleles (in trans) (PMID: 10441569); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 32573669, 10441569) -
Synaptic congenital myasthenic syndromes Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at