rs483352905

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM4_SupportingPP5_Moderate

The ENST00000340855.11(IDS):​c.349_351del​(p.Ser117del) variant causes a inframe deletion 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 Pathogenic (★).

Frequency

Genomes: not found (cov: 22)

Consequence

IDS
ENST00000340855.11 inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, single submitter P:2

Conservation

PhyloP100: 9.42
Variant links:
Genes affected
IDS (HGNC:5389): (iduronate 2-sulfatase) This gene encodes a member of the sulfatase family of proteins. The encoded preproprotein is proteolytically processed to generate two polypeptide chains. This enzyme is involved in the lysosomal degradation of heparan sulfate and dermatan sulfate. Mutations in this gene are associated with the X-linked lysosomal storage disease mucopolysaccharidosis type II, also known as Hunter syndrome. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PM1
In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in ENST00000340855.11
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in ENST00000340855.11. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant X-149503378-TGGA-T is Pathogenic according to our data. Variant chrX-149503378-TGGA-T is described in ClinVar as [Pathogenic]. Clinvar id is 10501.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-149503378-TGGA-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IDSNM_000202.8 linkuse as main transcriptc.349_351del p.Ser117del inframe_deletion 3/9 ENST00000340855.11 NP_000193.1
IDSNM_001166550.4 linkuse as main transcriptc.79_81del p.Ser27del inframe_deletion 3/9 NP_001160022.1
IDSNM_006123.5 linkuse as main transcriptc.349_351del p.Ser117del inframe_deletion 3/8 NP_006114.1
IDSNR_104128.2 linkuse as main transcriptn.518_520del non_coding_transcript_exon_variant 3/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IDSENST00000340855.11 linkuse as main transcriptc.349_351del p.Ser117del inframe_deletion 3/91 NM_000202.8 ENSP00000339801 P1P22304-1

Frequencies

GnomAD3 genomes
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
22

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Mucopolysaccharidosis, MPS-II Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMNov 29, 2001- -
Pathogenic, criteria provided, single submitterliterature onlyLaboratory of Diagnosis and Therapy of Lysosomal Disorders, University of PadovaJun 07, 2024In vitro or in vivo functional studies supportive of a damaging effect (PS3_Moderate), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Protein length changes in a nonrepeat region or stop–loss variants (PM4_Strong), Multiple lines of computational evidence support a deleterious effect (PP3_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Moderate) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs483352905; hg19: chrX-148584908; API