5-149368477-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024028.4(PCYOX1L):c.1308G>T(p.Arg436Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000229 in 1,613,116 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCYOX1L | NM_024028.4 | c.1308G>T | p.Arg436Ser | missense_variant | 6/6 | ENST00000274569.9 | |
PCYOX1L | NM_001301054.2 | c.1257G>T | p.Arg419Ser | missense_variant | 6/6 | ||
PCYOX1L | NM_001301057.2 | c.1080G>T | p.Arg360Ser | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCYOX1L | ENST00000274569.9 | c.1308G>T | p.Arg436Ser | missense_variant | 6/6 | 2 | NM_024028.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250152Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135128
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1460920Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726654
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152196Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 21, 2022 | The c.1308G>T (p.R436S) alteration is located in exon 6 (coding exon 6) of the PCYOX1L gene. This alteration results from a G to T substitution at nucleotide position 1308, causing the arginine (R) at amino acid position 436 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