5-149366111-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024028.4(PCYOX1L):c.640C>T(p.Arg214Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,764 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 (★).
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.640C>T | p.Arg214Trp | missense_variant | Exon 4 of 6 | ENST00000274569.9 | NP_076933.3 | |
PCYOX1L | NM_001301054.2 | c.589C>T | p.Arg197Trp | missense_variant | Exon 4 of 6 | NP_001287983.1 | ||
PCYOX1L | NM_001301057.2 | c.420-8C>T | splice_region_variant, intron_variant | Intron 3 of 5 | NP_001287986.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250446Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135508
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461420Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 727020
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.640C>T (p.R214W) alteration is located in exon 4 (coding exon 4) of the PCYOX1L gene. This alteration results from a C to T substitution at nucleotide position 640, causing the arginine (R) at amino acid position 214 to be replaced by a tryptophan (W). 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