rs759188040
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The ENST00000265641.10(CPT1A):āc.557A>Gā(p.Tyr186Cys) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,656 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000265641.10 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.557A>G | p.Tyr186Cys | missense_variant, splice_region_variant | 6/19 | ENST00000265641.10 | NP_001867.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.557A>G | p.Tyr186Cys | missense_variant, splice_region_variant | 6/19 | 1 | NM_001876.4 | ENSP00000265641 | P1 | |
CPT1A | ENST00000376618.6 | c.557A>G | p.Tyr186Cys | missense_variant, splice_region_variant | 6/19 | 1 | ENSP00000365803 | |||
CPT1A | ENST00000540367.5 | c.557A>G | p.Tyr186Cys | missense_variant, splice_region_variant | 5/18 | 1 | ENSP00000439084 | |||
CPT1A | ENST00000539743.5 | c.557A>G | p.Tyr186Cys | missense_variant, splice_region_variant | 5/18 | 5 | ENSP00000446108 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251394Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461612Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727136
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152044Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74266
ClinVar
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 28, 2019 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 25, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at