Genetic Variant PCYOX1L:p.Pro6Leu (chr5-149358085-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001301054.2(PCYOX1L):c.-51C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 1,280,880 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000062 ( 0 hom. )

Consequence

PCYOX1L
NM_001301054.2 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.82

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.036952943).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001301054.2. 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.17C>T	p.Pro6Leu	missense	Exon 1 of 6	NP_076933.3
PCYOX1L	NM_001301054.2		c.-51C>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 6	NP_001287983.1
PCYOX1L	NM_001301057.2		c.-51C>T		5_prime_UTR_premature_start_codon_gain	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.17C>T	p.Pro6Leu	missense	Exon 1 of 6	ENSP00000274569.4	Q8NBM8-1
PCYOX1L	ENST00000505669.5	TSL:1	n.17C>T		non_coding_transcript_exon	Exon 1 of 6	ENSP00000427166.1	Q8NBM8-2
PCYOX1L	ENST00000511945.5	TSL:1	n.17C>T		non_coding_transcript_exon	Exon 1 of 6	ENSP00000426091.1	Q8NBM8-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.0000155

AC:

AN:

64426

AF XY:

0.0000268

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000625

AC:

AN:

1280880

Hom.:

Cov.:

AF XY:

0.00000953

AC XY:

AN XY:

629758

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

26150

American (AMR)

AF:

0.00

AC:

AN:

23364

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

21498

East Asian (EAS)

AF:

0.0000728

AC:

AN:

27456

South Asian (SAS)

AF:

0.0000150

AC:

AN:

66692

European-Finnish (FIN)

AF:

0.00

AC:

AN:

32162

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3746

European-Non Finnish (NFE)

AF:

0.00000487

AC:

AN:

1027020

Other (OTH)

AF:

0.00

AC:

AN:

52792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000151

Asia WGS

AF:

0.000578

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.17

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.040

(source)

DANN

Benign

0.83

DEOGEN2

Benign

0.0015

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.056

LIST_S2

Benign

0.45

M_CAP

Benign

0.043

MetaRNN

Benign

0.037

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

PhyloP100

-2.8

PrimateAI

Uncertain

0.67

PROVEAN

Benign

0.48

REVEL

Benign

0.010

Sift

Benign

0.49

Sift4G

Benign

0.74

Polyphen

0.0

Vest4

0.052

MVP

0.076

MPC

0.19

ClinPred

0.030

GERP RS

-5.2

PromoterAI

0.18

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.020

gMVP

0.15

Mutation Taster

=93/7

polymorphism

(source)

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over