X-149498202-C-T
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM2PP3_ModeratePP5_Very_Strong
The NM_000202.8(IDS):c.613G>A(p.Ala205Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000273 in 1,097,556 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_000202.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IDS | NM_000202.8 | c.613G>A | p.Ala205Thr | missense_variant | Exon 5 of 9 | ENST00000340855.11 | NP_000193.1 | |
IDS | NM_001166550.4 | c.343G>A | p.Ala115Thr | missense_variant | Exon 5 of 9 | NP_001160022.1 | ||
IDS | NM_006123.5 | c.613G>A | p.Ala205Thr | missense_variant | Exon 5 of 8 | NP_006114.1 | ||
IDS | NR_104128.2 | n.782G>A | non_coding_transcript_exon_variant | Exon 5 of 9 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1097556Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 362912
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-II Pathogenic:3
Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Moderate), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Missense variant in a gene with a low rate of benign missense variation (PP2_Supporting), Multiple lines of computational evidence support a deleterious effect (PP3_Supporting), Patient’s phenotype or family history highly specific for the disease (PP4_Strong) -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at