5-149364150-A-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024028.4(PCYOX1L):āc.410A>Cā(p.Tyr137Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024028.4 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.410A>C | p.Tyr137Ser | missense_variant | 3/6 | ENST00000274569.9 | NP_076933.3 | |
PCYOX1L | NM_001301054.2 | c.359A>C | p.Tyr120Ser | missense_variant | 3/6 | NP_001287983.1 | ||
PCYOX1L | NM_001301057.2 | c.359A>C | p.Tyr120Ser | missense_variant | 3/6 | NP_001287986.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461870Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727236
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.410A>C (p.Y137S) alteration is located in exon 3 (coding exon 3) of the PCYOX1L gene. This alteration results from a A to C substitution at nucleotide position 410, causing the tyrosine (Y) at amino acid position 137 to be replaced by a serine (S). 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