11-74492359-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144869.3(LIPT2):c.472C>T(p.Arg158Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000451 in 1,550,562 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.472C>T | p.Arg158Cys | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.510C>T | p.Ser170Ser | synonymous_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.243C>T | p.Ser81Ser | synonymous_variant | Exon 2 of 2 | NP_001316871.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LIPT2 | ENST00000310109.5 | c.472C>T | p.Arg158Cys | missense_variant | Exon 2 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2 | ENST00000527115.1 | c.120C>T | p.Ser40Ser | synonymous_variant | Exon 2 of 2 | 2 | ENSP00000431210.1 | |||
LIPT2 | ENST00000528085.1 | c.186C>T | p.Ser62Ser | synonymous_variant | Exon 2 of 2 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000358 AC: 5AN: 1398438Hom.: 0 Cov.: 33 AF XY: 0.00000145 AC XY: 1AN XY: 689802
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 158 of the LIPT2 protein (p.Arg158Cys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LIPT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 2187954). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at