ClinVar Miner

Submissions for variant NM_182760.4(SUMF1):c.860A>T (p.Asn287Ile)

dbSNP: rs766298096
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics RCV001797855 SCV002039189 likely pathogenic Multiple sulfatase deficiency 2020-12-28 criteria provided, single submitter clinical testing A homozygous missense variation in exon 7 of the SUMF1 gene that results in the amino acid substitution of Isoleucine for Asparagine at codon 287 was detected. The observed variant c.860A>T (p.Asn287Ile) has not been reported in the 1000 genomes and gnomAD database. The in silico prediction of the variant are possibly damaging by PolyPhen-2 (HumDiv) and damaging by SIFT. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as a likely pathogenic variant.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004690133 SCV005184953 uncertain significance not specified 2024-05-09 criteria provided, single submitter clinical testing Variant summary: SUMF1 c.860A>T (p.Asn287Ile) results in a non-conservative amino acid change located in the sulfatase-modifying factor enzyme domain (IPR005532) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251118 control chromosomes. c.860A>T has been reported in the literature as homozygous in one individual affected with Multiple Sulfatase Deficiency (Sheth_2023). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 36959582). ClinVar contains an entry for this variant (Variation ID: 1328964). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001797855 SCV005660003 likely pathogenic Multiple sulfatase deficiency 2024-05-16 criteria provided, single submitter clinical testing

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