Variant rs2706762 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016297.4(PCYOX1):c.446C>T(p.Ser149Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 1,611,022 control chromosomes in the GnomAD database, including 14,876 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.095 ( 903 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13973 hom. )

Consequence

PCYOX1
NM_016297.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.08

Variant links:

Genes affected

PCYOX1 (HGNC:20588): (prenylcysteine oxidase 1) Prenylcysteine is released during the degradation of prenylated proteins. PCYOX1 catalyzes the degradation of prenylcysteine to yield free cysteines and a hydrophobic isoprenoid product (Tschantz et al., 1999 [PubMed 10585463]).[supplied by OMIM, Mar 2008]

PCYOX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019338727).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCYOX1	NM_016297.4 linkuse as main transcript	c.446C>T	p.Ser149Phe	missense_variant	3/6	ENST00000433351.7	NP_057381.3
PCYOX1	XM_047444689.1 linkuse as main transcript	c.215C>T	p.Ser72Phe	missense_variant	3/6		XP_047300645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCYOX1	ENST00000433351.7 linkuse as main transcript	c.446C>T	p.Ser149Phe	missense_variant	3/6	1	NM_016297.4	ENSP00000387654	P1	Q9UHG3-1

Frequencies

GnomAD3 genomes

AF:

0.0948

AC:

14415

AN:

152110

Hom.:

903

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0252

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.0749

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0806

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.0977

GnomAD3 exomes

AF:

0.0985

AC:

24775

AN:

251428

Hom.:

1540

AF XY:

0.103

AC XY:

13937

AN XY:

135900

show subpopulations

Gnomad AFR exome

AF:

0.0229

Gnomad AMR exome

AF:

0.0535

Gnomad ASJ exome

AF:

0.155

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.0826

Gnomad FIN exome

AF:

0.0635

Gnomad NFE exome

AF:

0.144

Gnomad OTH exome

AF:

0.118

GnomAD4 exome

AF:

0.131

AC:

191150

AN:

1458794

Hom.:

13973

Cov.:

AF XY:

0.131

AC XY:

94949

AN XY:

725930

show subpopulations

Gnomad4 AFR exome

AF:

0.0204

Gnomad4 AMR exome

AF:

0.0569

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0860

Gnomad4 FIN exome

AF:

0.0678

Gnomad4 NFE exome

AF:

0.149

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.0946

AC:

14402

AN:

152228

Hom.:

903

Cov.:

AF XY:

0.0890

AC XY:

6624

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0251

Gnomad4 AMR

AF:

0.0748

Gnomad4 ASJ

AF:

0.155

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0805

Gnomad4 FIN

AF:

0.0626

Gnomad4 NFE

AF:

0.150

Gnomad4 OTH

AF:

0.0957

Alfa

AF:

0.138

Hom.:

3793

Bravo

AF:

0.0918

TwinsUK

AF:

0.142

AC:

526

ALSPAC

AF:

0.147

AC:

568

ESP6500AA

AF:

0.0313

AC:

138

ESP6500EA

AF:

0.152

AC:

1309

ExAC

AF:

0.0997

AC:

12103

Asia WGS

AF:

0.0380

AC:

133

AN:

3478

EpiCase

AF:

0.152

EpiControl

AF:

0.153

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.16

DEOGEN2

Benign

0.0042

T;T;T;.;T

Eigen

Benign

-0.47

Eigen_PC

Benign

-0.22

FATHMM_MKL

Benign

0.71

LIST_S2

Benign

0.75

T;T;T;T;T

MetaRNN

Benign

0.0019

T;T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-0.53

.;.;N;.;.

MutationTaster

Benign

0.25

P;P;P;P

PrimateAI

Benign

0.40

PROVEAN

Benign

2.2

N;N;N;N;N

REVEL

Benign

0.19

Sift

Benign

1.0

T;T;T;T;T

Sift4G

Benign

0.13

T;T;T;T;T

Polyphen

0.0

.;.;B;.;.

Vest4

0.049, 0.039

MPC

0.088

ClinPred

0.016

GERP RS

4.6

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.042

gMVP

0.79

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over