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

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

PCYOX1L
NM_024028.4 missense

Scores

1
10
8

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.46
Variant links:
Genes affected
PCYOX1L (HGNC:28477): (prenylcysteine oxidase 1 like) Predicted to enable prenylcysteine oxidase activity. Predicted to be involved in prenylated protein catabolic process. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCYOX1LNM_024028.4 linkc.310C>T p.Arg104Cys missense_variant 3/6 ENST00000274569.9 NP_076933.3 Q8NBM8-1
PCYOX1LNM_001301054.2 linkc.259C>T p.Arg87Cys missense_variant 3/6 NP_001287983.1 Q8NBM8
PCYOX1LNM_001301057.2 linkc.259C>T p.Arg87Cys missense_variant 3/6 NP_001287986.1 Q8NBM8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCYOX1LENST00000274569.9 linkc.310C>T p.Arg104Cys missense_variant 3/62 NM_024028.4 ENSP00000274569.4 Q8NBM8-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461614
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
727092
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 16, 2024The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.40
CADD
Pathogenic
30
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.041
T;.
Eigen
Uncertain
0.43
Eigen_PC
Uncertain
0.48
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.95
D;D
M_CAP
Benign
0.021
T
MetaRNN
Uncertain
0.51
D;D
MetaSVM
Benign
-1.2
T
MutationAssessor
Uncertain
2.0
M;.
PrimateAI
Uncertain
0.67
T
PROVEAN
Uncertain
-3.0
D;D
REVEL
Benign
0.085
Sift
Uncertain
0.017
D;D
Sift4G
Uncertain
0.015
D;D
Polyphen
0.99
D;P
Vest4
0.75
MutPred
0.40
Gain of sheet (P = 0.0221);.;
MVP
0.25
MPC
0.82
ClinPred
0.99
D
GERP RS
5.7
Varity_R
0.24
gMVP
0.77

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs142255736; hg19: chr5-148743613; API