Submissions for variant NM_000202.8(IDS):c.104-2A>G

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Total submissions: 5

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova	RCV001782283	SCV005089101	pathogenic	Mucopolysaccharidosis, MPS-II	2024-06-07	criteria provided, single submitter	literature only	Null variant (PVS1_VeryStrong), Prevalence of the variant significantly increased in affected individuals compared with controls (PS4_Supporting), Absent from controls (or at low frequency) in gnomAD database (PM2_Moderate), Patient’s phenotype or family history highly specific for the disease (PP4_Moderate)
Labcorp Genetics (formerly Invitae), Labcorp	RCV001782283	SCV004298744	pathogenic	Mucopolysaccharidosis, MPS-II	2024-01-04	criteria provided, single submitter	clinical testing	This sequence change affects an acceptor splice site in intron 1 of the IDS gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in IDS are known to be pathogenic (PMID: 8940265, 9875019). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with mucopolysaccharidosis II (PMID: 33676511). This variant is also known as 228–2A>G. ClinVar contains an entry for this variant (Variation ID: 1324563). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV001782283	SCV003806923	pathogenic	Mucopolysaccharidosis, MPS-II	2021-05-20	criteria provided, single submitter	clinical testing	ACMG classification criteria: PVS1 very strong, PS4 supporting, PM2
Revvity Omics, Revvity	RCV001782283	SCV002016663	likely pathogenic	Mucopolysaccharidosis, MPS-II	2022-01-11	criteria provided, single submitter	clinical testing
Dr. Peter K. Rogan Lab, Western University	RCV005922463	SCV006994702	not provided	Nonpapillary renal cell carcinoma		no classification provided	in vitro

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