11-74493463-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144869.3(LIPT2):c.241C>T(p.Arg81Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000121 in 1,485,230 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LIPT2 | NM_001144869.3 | c.241C>T | p.Arg81Cys | missense_variant | Exon 1 of 2 | ENST00000310109.5 | NP_001138341.1 | |
LIPT2 | NM_001329941.2 | c.241C>T | p.Arg81Cys | missense_variant | Exon 1 of 2 | NP_001316870.1 | ||
LIPT2 | NM_001329942.2 | c.237+4C>T | splice_region_variant, intron_variant | Intron 1 of 1 | NP_001316871.1 | |||
LIPT2-AS1 | NR_171028.1 | n.84G>A | 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.241C>T | p.Arg81Cys | missense_variant | Exon 1 of 2 | 2 | NM_001144869.3 | ENSP00000309463.4 | ||
LIPT2-AS1 | ENST00000526036.1 | n.98G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 1 | |||||
LIPT2 | ENST00000528085.1 | c.180+4C>T | splice_region_variant, intron_variant | Intron 1 of 1 | 3 | ENSP00000433005.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000128 AC: 17AN: 1333060Hom.: 0 Cov.: 44 AF XY: 0.00000914 AC XY: 6AN XY: 656726
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.241C>T (p.R81C) alteration is located in exon 1 (coding exon 1) of the LIPT2 gene. This alteration results from a C to T substitution at nucleotide position 241, causing the arginine (R) at amino acid position 81 to be replaced by a cysteine (C). 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