5-149364050-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_024028.4(PCYOX1L):c.310C>T(p.Arg104Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,614 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.310C>T | p.Arg104Cys | missense_variant | Exon 3 of 6 | ENST00000274569.9 | NP_076933.3 | |
PCYOX1L | NM_001301054.2 | c.259C>T | p.Arg87Cys | missense_variant | Exon 3 of 6 | NP_001287983.1 | ||
PCYOX1L | NM_001301057.2 | c.259C>T | p.Arg87Cys | missense_variant | Exon 3 of 6 | NP_001287986.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461614Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727092
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.310C>T (p.R104C) alteration is located in exon 3 (coding exon 3) of the PCYOX1L gene. This alteration results from a C to T substitution at nucleotide position 310, causing the arginine (R) at amino acid position 104 to be replaced by a cysteine (C). 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