rs1554086417

Variant names:

• chr5-78955439-AGTAT-CTTCAGG
• rs1554086417
• NM_000046.5:c.750_754delATACTinsCCTGAAG

Your query was ambiguous. Multiple possible variants found:

• chr5-78955438-AAGTAT-ACTTCAGG
• chr5-78955438-AAGTAT-ACTTGACTTCAGG

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000046.5(ARSB):​c.750_754delATACTinsCCTGAAG​(p.Glu250AspfsTer4) variant causes a frameshift, missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. E250E) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 33)
• Consequence: ARSB NM_000046.5 frameshift, missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.87

Genes affected

ARSB (HGNC:714): (arylsulfatase B) Arylsulfatase B encoded by this gene belongs to the sulfatase family. The arylsulfatase B homodimer hydrolyzes sulfate groups of N-Acetyl-D-galactosamine, chondriotin sulfate, and dermatan sulfate. The protein is targeted to the lysozyme. Mucopolysaccharidosis type VI is an autosomal recessive lysosomal storage disorder resulting from a deficiency of arylsulfatase B. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-78955439-AGTAT-CTTCAGG is Pathogenic according to our data. Variant chr5-78955439-AGTAT-CTTCAGG is described in ClinVar as [Likely_pathogenic]. Clinvar id is 559810.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ARSB	NM_000046.5	c.750_754delATACTinsCCTGAAG	p.Glu250AspfsTer4	frameshift_variant, missense_variant	Exon 4 of 8	ENST00000264914.10	NP_000037.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ARSB	ENST00000264914.10	c.750_754delATACTinsCCTGAAG	p.Glu250AspfsTer4	frameshift_variant, missense_variant	Exon 4 of 8	1	NM_000046.5	ENSP00000264914.4
ARSB	ENST00000396151.7	c.750_754delATACTinsCCTGAAG	p.Glu250AspfsTer4	frameshift_variant, missense_variant	Exon 5 of 8	1		ENSP00000379455.3
ARSB	ENST00000565165.2	c.750_754delATACTinsCCTGAAG	p.Glu250AspfsTer4	frameshift_variant, missense_variant	Exon 4 of 5	1		ENSP00000456339.2
ARSB	ENST00000521800.2	n.-69_-65delATACTinsCCTGAAG		upstream_gene_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mucopolysaccharidosis type 6 Pathogenic:1

Jan 01, 2018

Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

Frameshift variant (PVS1); Absent from GnomAD (PM2) -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554086417; hg19: chr5-78251262;