5-149358085-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_024028.4(PCYOX1L):​c.17C>G​(p.Pro6Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0005 in 1,433,036 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P6Q) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.00056 ( 1 hom., cov: 33)
Exomes š‘“: 0.00049 ( 2 hom. )

Consequence

PCYOX1L
NM_024028.4 missense

Scores

1
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.82
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 Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0034115314).
BS2
High Homozygotes in GnomAdExome4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PCYOX1LNM_024028.4 linkc.17C>G p.Pro6Arg missense_variant Exon 1 of 6 ENST00000274569.9 NP_076933.3 Q8NBM8-1
PCYOX1LNM_001301054.2 linkc.-51C>G 5_prime_UTR_variant Exon 1 of 6 NP_001287983.1 Q8NBM8
PCYOX1LNM_001301057.2 linkc.-51C>G 5_prime_UTR_variant Exon 1 of 6 NP_001287986.1 Q8NBM8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PCYOX1LENST00000274569.9 linkc.17C>G p.Pro6Arg missense_variant Exon 1 of 6 2 NM_024028.4 ENSP00000274569.4 Q8NBM8-1
PCYOX1LENST00000505669.5 linkn.17C>G non_coding_transcript_exon_variant Exon 1 of 6 1 ENSP00000427166.1 Q8NBM8-2
PCYOX1LENST00000511945.5 linkn.17C>G non_coding_transcript_exon_variant Exon 1 of 6 1 ENSP00000426091.1 Q8NBM8-2
PCYOX1LENST00000510990.6 linkn.17C>G non_coding_transcript_exon_variant Exon 1 of 5 4 ENSP00000422063.2 D6R9J0

Frequencies

GnomAD3 genomes
AF:
0.000559
AC:
85
AN:
152060
Hom.:
1
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.0188
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00318
Gnomad NFE
AF:
0.000235
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00196
AC:
126
AN:
64426
Hom.:
0
AF XY:
0.00180
AC XY:
67
AN XY:
37284
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.0195
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000506
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000388
Gnomad OTH exome
AF:
0.00268
GnomAD4 exome
AF:
0.000493
AC:
632
AN:
1280864
Hom.:
2
Cov.:
31
AF XY:
0.000480
AC XY:
302
AN XY:
629750
show subpopulations
Gnomad4 AFR exome
AF:
0.0000382
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.0204
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000195
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000100
Gnomad4 OTH exome
AF:
0.00140
GnomAD4 genome
AF:
0.000559
AC:
85
AN:
152172
Hom.:
1
Cov.:
33
AF XY:
0.000618
AC XY:
46
AN XY:
74410
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.0188
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000235
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.00292
Hom.:
0
Bravo
AF:
0.000548
ExAC
AF:
0.00148
AC:
21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.62
T
BayesDel_noAF
Benign
-0.79
CADD
Benign
0.076
DANN
Benign
0.58
DEOGEN2
Benign
0.00084
T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.038
N
LIST_S2
Benign
0.37
T
MetaRNN
Benign
0.0034
T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
0.0
N
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-0.16
N
REVEL
Benign
0.010
Sift
Benign
0.58
T
Sift4G
Benign
0.57
T
Polyphen
0.0
B
Vest4
0.10
MutPred
0.43
Gain of MoRF binding (P = 0);
MVP
0.067
MPC
0.19
ClinPred
0.0045
T
GERP RS
-5.2
Varity_R
0.025
gMVP
0.26

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: rs760672430; hg19: chr5-148737648; API