chrX-153862663-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM4PP5_Moderate
The NM_001278116.2(L1CAM):c.3774G>C(p.Ter1258TyrextTer264) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. *1258*) has been classified as Likely benign.
Frequency
Consequence
NM_001278116.2 stop_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
L1CAM | NM_001278116.2 | c.3774G>C | p.Ter1258TyrextTer264 | stop_lost | 29/29 | ENST00000370060.7 | |
L1CAM | NM_000425.5 | c.3774G>C | p.Ter1258TyrextTer264 | stop_lost | 28/28 | ||
L1CAM | NM_024003.3 | c.3762G>C | p.Ter1254TyrextTer264 | stop_lost | 27/27 | ||
L1CAM | NM_001143963.2 | c.3747G>C | p.Ter1249TyrextTer264 | stop_lost | 26/26 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
L1CAM | ENST00000370060.7 | c.3774G>C | p.Ter1258TyrextTer264 | stop_lost | 29/29 | 5 | NM_001278116.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 28
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 06, 2017 | The c.3774 G>C variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The c.3774 G>C missense variant alters the stop codon at position 1258, changing it to a Tyrosine and extending the protein's C-terminus, with a new stop codon at position 264, denoted p.X1258TyrextX264. This variant is predicted to cause protein extension by adding 264 incorrect amino acids. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at