rs863224892
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_145199.3(LIPT1):c.806G>A(p.Trp269*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_145199.3 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT1 | ENST00000651691.1 | c.806G>A | p.Trp269* | stop_gained | Exon 2 of 2 | NM_145199.3 | ENSP00000498546.1 | |||
ENSG00000273155 | ENST00000410042.1 | c.-28+6337G>A | intron_variant | Intron 2 of 5 | 2 | ENSP00000387111.1 | ||||
ENSG00000241962 | ENST00000424491.5 | n.63+12244G>A | intron_variant | Intron 4 of 13 | 2 | ENSP00000390891.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Lipoyl transferase 1 deficiency Pathogenic:1
The stop gained variant c.806G>A (p.Trp269Ter) in LIPT1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant has not been reported to the ClinVar database.The variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The nucleotide change in LIPT1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at