rs201562892

Variant names:

• chr22-50487968-C-A
• rs201562892
• NM_017584.6:c.260C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-50487968-C-A
• chr22-50487968-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_017584.6(MIOX):​c.260C>A​(p.Ser87*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MIOX NM_017584.6 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.94

Genes affected

MIOX (HGNC:14522): (myo-inositol oxygenase) Enables ferric iron binding activity and inositol oxygenase activity. Involved in inositol catabolic process. Predicted to be located in cytoplasm and inclusion body. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIOX	NM_017584.6	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 10	ENST00000216075.11	NP_060054.4
MIOX	XM_005261925.5	c.122C>A	p.Ser41*	stop_gained	Exon 3 of 9		XP_005261982.1
MIOX	XM_011530705.3	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 6		XP_011529007.1
MIOX	XM_047441443.1	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 9		XP_047297399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIOX	ENST00000216075.11	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 10	1	NM_017584.6	ENSP00000216075.6
MIOX	ENST00000395732.7	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 10	1		ENSP00000379081.3
MIOX	ENST00000395733.7	c.260C>A	p.Ser87*	stop_gained	Exon 4 of 8	1		ENSP00000379082.3
MIOX	ENST00000451761.1	c.245C>A	p.Ser82*	stop_gained	Exon 3 of 9	3		ENSP00000409894.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.65
CADD	Pathogenic	39
DANN	Uncertain	0.99
Eigen	Pathogenic	0.70
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Pathogenic	0.97	D
Vest4		0.81
GERP RS		4.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs201562892; hg19: chr22-50926397;