chrX-130631531-A-T

Variant names:

• chrX-130631531-A-T
• rs371121524
• NM_006375.4:c.1465T>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006375.4(ENOX2):​c.1465T>A​(p.Tyr489Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. Y489H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: ENOX2 NM_006375.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 0 publications found

Genes affected

ENOX2 (HGNC:2259): (ecto-NOX disulfide-thiol exchanger 2) This gene is a tumor-specific member of the ECTO-NOX family of genes that encode cell surface NADH oxidases. The encoded protein has two enzymatic activities: catalysis of hydroquinone or NADH oxidation, and protein disulfide interchange. The protein also displays prion-like properties. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

ACMG classification

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=0.11148226).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006375.4. 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
	ENOX2	NM_006375.4	MANE Select	c.1465T>A	p.Tyr489Asn	missense	Exon 13 of 15	NP_006366.2
	ENOX2	NM_001382518.1		c.1741T>A	p.Tyr581Asn	missense	Exon 14 of 16	NP_001369447.1	A0A8I5KRI1
	ENOX2	NM_001382516.1		c.1552T>A	p.Tyr518Asn	missense	Exon 16 of 18	NP_001369445.1	Q16206-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENOX2	ENST00000394363.6	TSL:2 MANE Select	c.1465T>A	p.Tyr489Asn	missense	Exon 13 of 15	ENSP00000377890.1	Q16206-2
	ENOX2	ENST00000370927.5	TSL:1	c.1552T>A	p.Tyr518Asn	missense	Exon 11 of 13	ENSP00000359965.1	Q16206-1
	ENOX2	ENST00000686943.1		c.1741T>A	p.Tyr581Asn	missense	Exon 14 of 16	ENSP00000509235.1	A0A8I5KRI1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 23

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ESP6500AA AF: 0.000261 AC: 1

ESP6500EA AF: 0.00 AC: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.72
DEOGEN2	Benign	0.051	T
FATHMM_MKL	Benign	0.11	N
LIST_S2	Benign	0.81	T
M_CAP	Benign	0.0095	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	-0.34	N
PhyloP100		0.50
PrimateAI	Benign	0.39	T
PROVEAN	Benign	0.69	N
REVEL	Benign	0.099
Sift	Benign	0.49	T
Sift4G	Benign	0.42	T
Polyphen		0.0	B
Vest4		0.35
MVP		0.64
MPC		0.28
ClinPred		0.076	T
GERP RS		3.4
Varity_R		0.067
gMVP		0.084
Mutation Taster		=99/1	polymorphism

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

Other links and lift over

dbSNP: rs371121524; hg19: chrX-129765505;