11-74492340-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001144869.3(LIPT2):c.491C>T(p.Thr164Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000114 in 1,399,386 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 (★).
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.491C>T | p.Thr164Ile | missense_variant | Exon 2 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.529C>T | p.His177Tyr | missense_variant | Exon 2 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.262C>T | p.His88Tyr | 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.491C>T | p.Thr164Ile | missense_variant | Exon 2 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2 | ENST00000527115.1 | c.139C>T | p.His47Tyr | missense_variant | Exon 2 of 2 | 2 | ENSP00000431210.1 | |||
LIPT2 | ENST00000528085.1 | c.205C>T | p.His69Tyr | missense_variant | Exon 2 of 2 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000114 AC: 16AN: 1399386Hom.: 0 Cov.: 34 AF XY: 0.0000130 AC XY: 9AN XY: 690206
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.491C>T (p.T164I) alteration is located in exon 2 (coding exon 2) of the LIPT2 gene. This alteration results from a C to T substitution at nucleotide position 491, causing the threonine (T) at amino acid position 164 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at