5-146120383-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_020117.11(LARS1):c.3313C>T(p.Arg1105*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000093 in 1,612,694 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 Likely pathogenic (★★).
Frequency
Consequence
NM_020117.11 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151974Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250994Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135648
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460720Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726628
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151974Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74236
ClinVar
Submissions by phenotype
not provided Pathogenic:2
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Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins Pathogenic:1
Variant summary: LARS c.3313C>T (p.Arg1105X) results in a premature termination codon, predicted to cause a truncation of the encoded protein. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 2e-05 in 250994 control chromosomes (gnomAD). c.3313C>T has been reported in the literature as a homozygous genotype in two siblings affected with Liver Failure Acute Infantile, Type 1 (e.g. Lenz_2020). These data indicate that the variant is likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact of the variant on protein function in fibroblasts derived from a homozygous patient (e.g. Lenz_2020). The variant resulted in a truncated protein product but did not appear to undergo nonsense mediated decay. The protein showed reduced enzymatic activity, approximately 70% of normal, which was further reduced at higher temperatures to approximately 45% of normal, likely as a result of reduced protein stability, as indicated by a reduced expression at higher temperatures evaluated by western blotting. Three submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as either pathogenic (n=2) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
Infantile liver failure syndrome 1 Pathogenic:1
This variant was identified as homozygous. -
LARS1-related disorder Pathogenic:1
This nonsense variant found in exon 31 of 32 is predicted to result in protein truncation. This variant has been previously reported as a homozygous change in two related individuals with features of infantile liver failure syndrome 1 (ILFS1), however both were noted to lack the episodic liver dysfunction that is typical of the disorder (PMID: 32699352). Experimental studies have shown that the presence of the c.3313C>T (p.Arg1105Ter) variant leads to reduced LARS1 enzyme activity, and that the variant likely causes truncation of the LARS1 protein (PMID: 32699352). The c.3313C>T (p.Arg1105Ter) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.002479% (7/282358) and is absent in the homozygous state. Based on the available evidence, the c.3313C>T (p.Arg1105Ter) variant is classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at