11-74492316-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001144869.3(LIPT2):āc.515G>Cā(p.Cys172Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000143 in 1,399,492 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 Uncertain significance (ā ).
Frequency
Consequence
NM_001144869.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.515G>C | p.Cys172Ser | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.553G>C | p.Ala185Pro | missense_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.286G>C | p.Ala96Pro | 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.515G>C | p.Cys172Ser | missense_variant | Exon 2 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2 | ENST00000527115.1 | c.163G>C | p.Ala55Pro | missense_variant | Exon 2 of 2 | 2 | ENSP00000431210.1 | |||
LIPT2 | ENST00000528085.1 | c.*12G>C | downstream_gene_variant | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000636 AC: 1AN: 157206Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 83210
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399492Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 690248
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Uncertain:1
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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with LIPT2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.004%). This sequence change replaces cysteine, which is neutral and slightly polar, with serine, which is neutral and polar, at codon 172 of the LIPT2 protein (p.Cys172Ser). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at