chr5-149366069-G-C

Variant names:

• chr5-149366069-G-C
• rs775307182
• NM_024028.4:c.598G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_024028.4(PCYOX1L):​c.598G>C​(p.Val200Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. V200I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: PCYOX1L NM_024028.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.80
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYOX1L	NM_024028.4	MANE Select	c.598G>C	p.Val200Leu	missense	Exon 4 of 6	NP_076933.3
	PCYOX1L	NM_001301054.2		c.547G>C	p.Val183Leu	missense	Exon 4 of 6	NP_001287983.1
	PCYOX1L	NM_001301057.2		c.420-50G>C		intron	N/A	NP_001287986.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PCYOX1L	ENST00000274569.9	TSL:2 MANE Select	c.598G>C	p.Val200Leu	missense	Exon 4 of 6	ENSP00000274569.4	Q8NBM8-1
	PCYOX1L	ENST00000507621.1	TSL:1	n.3001G>C		non_coding_transcript_exon	Exon 1 of 3
	PCYOX1L	ENST00000511945.5	TSL:1	n.*365G>C		non_coding_transcript_exon	Exon 4 of 6	ENSP00000426091.1	Q8NBM8-2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.62
BayesDel_addAF	Benign	-0.010	T
BayesDel_noAF	Benign	-0.25
CADD	Uncertain	23
DANN	Uncertain	1.0
DEOGEN2	Benign	0.00098	T
Eigen	Uncertain	0.26
Eigen_PC	Uncertain	0.35
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.91	D
M_CAP	Benign	0.014	T
MetaRNN	Uncertain	0.64	D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.5	M
PhyloP100		4.8
PrimateAI	Uncertain	0.58	T
PROVEAN	Benign	-0.020	N
REVEL	Benign	0.17
Sift	Benign	0.042	D
Sift4G	Benign	0.27	T
Polyphen		0.74	P
Vest4		0.66
MutPred		0.58		Gain of helix (P = 0.1736)
MVP		0.16
MPC		0.73
ClinPred		0.92	D
GERP RS		5.0
Varity_R		0.36
gMVP		0.70
Mutation Taster		=53/47	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs775307182; hg19: chr5-148745632;