rs770035560
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The ENST00000274680.9(FARS2):āc.253C>Gā(p.Pro85Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,888 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000274680.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.253C>G | p.Pro85Ala | missense_variant | 2/7 | ENST00000274680.9 | NP_006558.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.253C>G | p.Pro85Ala | missense_variant | 2/7 | 1 | NM_006567.5 | ENSP00000274680 | P1 | |
FARS2 | ENST00000324331.10 | c.253C>G | p.Pro85Ala | missense_variant | 2/7 | 1 | ENSP00000316335 | P1 | ||
FARS2 | ENST00000648580.1 | c.253C>G | p.Pro85Ala | missense_variant, NMD_transcript_variant | 2/9 | ENSP00000497889 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251294Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135852
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 14, 2021 | This variant has been reported to affect FARS2 protein function (PMID: 27095821). 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. This variant has been observed in combination with another FARS2 variant in an individual affected with juvenile onset refractory epilepsy and progressive myoclonus (PMID: 27095821). ClinVar contains an entry for this variant (Variation ID: 587669). This variant is present in population databases (rs770035560, ExAC 0.002%). This sequence change replaces proline with alanine at codon 85 of the FARS2 protein (p.Pro85Ala). The proline residue is highly conserved and there is a small physicochemical difference between proline and alanine. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jun 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at