16-55823661-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_001025195.2(CES1):c.428G>A(p.Gly143Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,886 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001025195.2 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 |
---|---|---|---|---|---|---|---|
CES1 | NM_001025195.2 | c.428G>A | p.Gly143Glu | missense_variant | 4/14 | ENST00000360526.8 | |
CES1 | NM_001025194.2 | c.425G>A | p.Gly142Glu | missense_variant | 4/14 | ||
CES1 | NM_001266.5 | c.425G>A | p.Gly142Glu | missense_variant | 4/14 | ||
CES1 | XM_005255774.3 | c.428G>A | p.Gly143Glu | missense_variant | 4/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CES1 | ENST00000360526.8 | c.428G>A | p.Gly143Glu | missense_variant | 4/14 | 1 | NM_001025195.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 39
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251250Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135802
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461708Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727166
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152178Hom.: 0 Cov.: 39 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
DRUG METABOLISM, ALTERED, CES1-RELATED Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at