11-74493390-A-C
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_001144869.3(LIPT2):c.314T>G(p.Leu105Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000198 in 1,515,072 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_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.314T>G | p.Leu105Arg | missense_variant | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.314T>G | p.Leu105Arg | missense_variant | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+77T>G | intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.11A>C | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT2 | ENST00000310109.5 | c.314T>G | p.Leu105Arg | missense_variant | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.25A>C | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+77T>G | intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 34
GnomAD4 exome AF: 7.34e-7 AC: 1AN: 1362864Hom.: 0 Cov.: 41 AF XY: 0.00 AC XY: 0AN XY: 672190
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74372
ClinVar
Submissions by phenotype
Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities Pathogenic:3
This variant is interpreted as a Likely Pathogenic, for Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities, Autosomal Recessive inheritance. The following ACMG Tag(s) were applied: PS3 => Well-established functional studies show a deleterious effect (PMID:28757203). PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product. PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:28757203). -
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not provided Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at