rs139805483
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_004461.3(FARSA):c.1040C>T(p.Pro347Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,606,256 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_004461.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000810 AC: 20AN: 246852Hom.: 0 AF XY: 0.0000749 AC XY: 10AN XY: 133508
GnomAD4 exome AF: 0.000127 AC: 184AN: 1453892Hom.: 0 Cov.: 34 AF XY: 0.000120 AC XY: 87AN XY: 722092
GnomAD4 genome AF: 0.000144 AC: 22AN: 152364Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74504
ClinVar
Submissions by phenotype
Rajab interstitial lung disease with brain calcifications 2 Pathogenic:1
This sequence change in FARSA is predicted to replace proline with leucine at codon 347, p.(Pro347Leu). The proline residue is highly conserved (100 vertebrates, UCSC), and is a residue located at the heterodimer interface in the AA tRNA Ligase II domain (PMID: 35918773). There is a moderate physicochemical difference between proline and leucine. The highest population minor allele frequency in gnomAD v2.1 is 0.02% (21/126,978 alleles) in the European (non-Finnish) population, which is consistent with recessive disease. This variant has been detected in at least two probands compound heterozygous with a variant of uncertain significance (confirmed in trans) with a systemic disorder that included failure to thrive, hepatic dysfunction and progressive interstitial lung disease, and segregated in two affected family members from a single family (PMID: 35918773, https://n.neurology.org/content/98/18_Supplement/1171). An in vitro assay of heterotetramerisation showed the variant failed to form a heteromer with FARSB indicating that this variant impacts protein function (PMID: 35918773). Multiple lines of computational evidence predict a deleterious effect for the missense substitution (5/6 algorithms). Based on the classification scheme RMH Modified ACMG Guidelines v1.5.1, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PS3_Supporting, PM1_Supporting, PM2_Supporting, PM3_Supporting, PP1, PP3. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at