11-74492285-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144869.3(LIPT2):āc.546C>Gā(p.Ile182Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,551,688 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.546C>G | p.Ile182Met | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.584C>G | p.Ser195Trp | missense_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.317C>G | p.Ser106Trp | missense_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.546C>G | p.Ile182Met | missense_variant | Exon 2 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2 | ENST00000527115.1 | c.194C>G | p.Ser65Trp | missense_variant | Exon 2 of 2 | 2 | ENSP00000431210.1 | |||
LIPT2 | ENST00000528085.1 | c.*43C>G | downstream_gene_variant | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000446 AC: 7AN: 156956Hom.: 0 AF XY: 0.0000481 AC XY: 4AN XY: 83118
GnomAD4 exome AF: 0.0000171 AC: 24AN: 1399506Hom.: 0 Cov.: 34 AF XY: 0.0000203 AC XY: 14AN XY: 690254
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 182 of the LIPT2 protein (p.Ile182Met). This variant is present in population databases (rs761309052, gnomAD 0.04%). 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: 1403856). 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