Genetic Variant PCYOX1L:p.Lys28Asn (chr5-149358152-A-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024028.4(PCYOX1L):c.84A>T(p.Lys28Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000767 in 1,303,180 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 7.7e-7 ( 0 hom. )

Consequence

PCYOX1L
NM_024028.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.20

Publications

0 publications found

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]

PCYOX1L links:

GRPEL2-AS1 (HGNC:48999): (GRPEL2 antisense RNA 1)

GRPEL2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.21765977).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024028.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
PCYOX1L	NM_024028.4	MANE Select	c.84A>T	p.Lys28Asn	missense	Exon 1 of 6	NP_076933.3
PCYOX1L	NM_001301054.2		c.17A>T	p.Lys6Ile	missense	Exon 1 of 6	NP_001287983.1
PCYOX1L	NM_001301057.2		c.17A>T	p.Lys6Ile	missense	Exon 1 of 6	NP_001287986.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PCYOX1L	ENST00000274569.9	TSL:2 MANE Select	c.84A>T	p.Lys28Asn	missense	Exon 1 of 6	ENSP00000274569.4	Q8NBM8-1
PCYOX1L	ENST00000505669.5	TSL:1	n.84A>T		non_coding_transcript_exon	Exon 1 of 6	ENSP00000427166.1	Q8NBM8-2
PCYOX1L	ENST00000511945.5	TSL:1	n.84A>T		non_coding_transcript_exon	Exon 1 of 6	ENSP00000426091.1	Q8NBM8-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000127

AC:

AN:

78702

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000460

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

7.67e-7

AC:

AN:

1303180

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

641918

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26520

American (AMR)

AF:

0.00

AC:

AN:

24984

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22890

East Asian (EAS)

AF:

0.0000358

AC:

AN:

27910

South Asian (SAS)

AF:

0.00

AC:

AN:

70460

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33988

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3818

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1038830

Other (OTH)

AF:

0.00

AC:

AN:

53780

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.67

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.53

CADD

Benign

(source)

DANN

Benign

0.94

DEOGEN2

Benign

0.0029

Eigen

Benign

0.074

Eigen_PC

Benign

0.080

FATHMM_MKL

Uncertain

0.89

LIST_S2

Benign

0.82

M_CAP

Benign

0.012

MetaRNN

Benign

0.22

MetaSVM

Benign

-1.1

PhyloP100

1.2

PrimateAI

Pathogenic

0.85

PROVEAN

Benign

-1.2

REVEL

Benign

0.13

Sift

Benign

0.088

Sift4G

Uncertain

0.0090

Polyphen

1.0

Vest4

0.34

MutPred

0.51

Loss of methylation at K28 (P = 0.0098)

MVP

0.35

MPC

0.21

ClinPred

0.85

GERP RS

2.6

PromoterAI

0.13

Neutral

(source)

Varity_R

0.10

gMVP

0.61

Mutation Taster

=61/39

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over