16-66995747-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001364782.1(CES4A):āc.178C>Gā(p.Pro60Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000568 in 1,461,884 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 (ā ).
Frequency
Consequence
NM_001364782.1 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 |
---|---|---|---|---|---|---|---|---|
CES4A | NM_001364782.1 | c.178C>G | p.Pro60Ala | missense_variant | Exon 2 of 14 | ENST00000648724.3 | NP_001351711.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CES4A | ENST00000648724.3 | c.178C>G | p.Pro60Ala | missense_variant | Exon 2 of 14 | NM_001364782.1 | ENSP00000497868.2 | |||
CES4A | ENST00000538199.5 | c.67C>G | p.Pro23Ala | missense_variant | Exon 1 of 11 | 1 | ENSP00000441103.1 | |||
CES4A | ENST00000540947.6 | c.178C>G | p.Pro60Ala | missense_variant | Exon 2 of 12 | 2 | ENSP00000444052.2 | |||
CES4A | ENST00000567587.6 | n.118C>G | non_coding_transcript_exon_variant | Exon 1 of 11 | 5 | ENSP00000458664.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000801 AC: 20AN: 249574Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135402
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.0000743 AC XY: 54AN XY: 727242
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.178C>G (p.P60A) alteration is located in exon 2 (coding exon 2) of the CES4A gene. This alteration results from a C to G substitution at nucleotide position 178, causing the proline (P) at amino acid position 60 to be replaced by an alanine (A). 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