Variant 5-149358115-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024028.4(PCYOX1L):c.47C>T(p.Ala16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000464 in 1,293,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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: 0.0000046 ( 0 hom. )

Consequence

PCYOX1L
NM_024028.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.97

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:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.057035953).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCYOX1L	NM_024028.4 linkuse as main transcript	c.47C>T	p.Ala16Val	missense_variant	1/6	ENST00000274569.9	NP_076933.3	Q8NBM8-1
PCYOX1L	NM_001301054.2 linkuse as main transcript	c.-21C>T		5_prime_UTR_variant	1/6		NP_001287983.1	Q8NBM8
PCYOX1L	NM_001301057.2 linkuse as main transcript	c.-21C>T		5_prime_UTR_variant	1/6		NP_001287986.1	Q8NBM8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
PCYOX1L	ENST00000274569.9 linkuse as main transcript	c.47C>T	p.Ala16Val	missense_variant	1/6	2	NM_024028.4	ENSP00000274569.4	Q8NBM8-1
PCYOX1L	ENST00000505669.5 linkuse as main transcript	n.47C>T		non_coding_transcript_exon_variant	1/6	1		ENSP00000427166.1	Q8NBM8-2
PCYOX1L	ENST00000511945.5 linkuse as main transcript	n.47C>T		non_coding_transcript_exon_variant	1/6	1		ENSP00000426091.1	Q8NBM8-2
PCYOX1L	ENST00000510990.6 linkuse as main transcript	n.47C>T		non_coding_transcript_exon_variant	1/5	4		ENSP00000422063.2	D6R9J0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000261

AC:

AN:

76666

Hom.:

AF XY:

0.0000227

AC XY:

AN XY:

44068

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 SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000194

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000457

GnomAD4 exome

AF:

0.00000464

AC:

AN:

1293138

Hom.:

Cov.:

AF XY:

0.00000471

AC XY:

AN XY:

636336

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000720

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000302

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000561

GnomAD4 genome

Cov.:

Asia WGS

AF:

0.000289

AC:

AN:

3478

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 submitter

clinical testing

Ambry Genetics

Apr 01, 2024

The c.47C>T (p.A16V) alteration is located in exon 1 (coding exon 1) of the PCYOX1L gene. This alteration results from a C to T substitution at nucleotide position 47, causing the alanine (A) at amino acid position 16 to be replaced by a valine (V). 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

0.18

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.0042

Eigen

Benign

-0.77

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.40

LIST_S2

Benign

0.53

M_CAP

Benign

0.011

MetaRNN

Benign

0.057

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.0

PrimateAI

Uncertain

0.76

PROVEAN

Benign

-0.13

REVEL

Benign

0.030

Sift

Benign

0.81

Sift4G

Benign

0.24

Polyphen

0.012

Vest4

0.26

MutPred

0.34

Loss of disorder (P = 0.0439);

MVP

0.076

MPC

0.18

ClinPred

0.083

GERP RS

3.3

Varity_R

0.063

gMVP

0.40

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over