rs483352905
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM4_SupportingPP5
The NM_000202.8(IDS):c.349_351del(p.Ser117del) variant causes a inframe deletion change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 22)
Consequence
IDS
NM_000202.8 inframe_deletion
NM_000202.8 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 9.42
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM1
?
In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in NM_000202.8
PM4
?
Nonframeshift variant in NON repetitive region in NM_000202.8. 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 no_assertion_criteria_provided, 0 stars. Variant chrX-149503378-TGGA-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDS | NM_000202.8 | c.349_351del | p.Ser117del | inframe_deletion | 3/9 | ENST00000340855.11 | |
IDS | NM_001166550.4 | c.79_81del | p.Ser27del | inframe_deletion | 3/9 | ||
IDS | NM_006123.5 | c.349_351del | p.Ser117del | inframe_deletion | 3/8 | ||
IDS | NR_104128.2 | n.518_520del | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDS | ENST00000340855.11 | c.349_351del | p.Ser117del | inframe_deletion | 3/9 | 1 | NM_000202.8 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Mucopolysaccharidosis, MPS-II Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 29, 2001 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at