rs869025303
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000202.8(IDS):āc.1025A>Gā(p.His342Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,981 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 (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H342P) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000202.8 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDS | NM_000202.8 | c.1025A>G | p.His342Arg | missense_variant | 8/9 | ENST00000340855.11 | |
IDS | NM_001166550.4 | c.755A>G | p.His252Arg | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDS | ENST00000340855.11 | c.1025A>G | p.His342Arg | missense_variant | 8/9 | 1 | NM_000202.8 | P1 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097981Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363337
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
Mucopolysaccharidosis, MPS-II Pathogenic:1
Likely pathogenic, criteria provided, single submitter | literature only | Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova | Jun 07, 2024 | Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Strong), 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) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at