rs28936374
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001876.4(CPT1A):c.2126G>A(p.Gly709Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,078 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G709R) has been classified as Uncertain significance.
Frequency
Consequence
NM_001876.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CPT1A | NM_001876.4 | c.2126G>A | p.Gly709Glu | missense_variant | 17/19 | ENST00000265641.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CPT1A | ENST00000265641.10 | c.2126G>A | p.Gly709Glu | missense_variant | 17/19 | 1 | NM_001876.4 | P1 | |
CPT1A | ENST00000376618.6 | c.2126G>A | p.Gly709Glu | missense_variant | 17/19 | 1 | |||
CPT1A | ENST00000540367.5 | c.2126G>A | p.Gly709Glu | missense_variant | 16/18 | 1 | |||
CPT1A | ENST00000539743.5 | c.2126G>A | p.Gly709Glu | missense_variant | 16/18 | 5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1458078Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725034
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Carnitine palmitoyl transferase 1A deficiency Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 12, 2003 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at