ClinVar Miner

Submissions for variant NM_022166.4(XYLT1):c.1588-3C>T

gnomAD frequency: 0.00132  dbSNP: rs201818754
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000960539 SCV001107530 likely benign Desbuquois dysplasia 1 2024-01-17 criteria provided, single submitter clinical testing
GeneDx RCV001553443 SCV001774313 likely benign not provided 2020-07-29 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 31589614, 30919572, 24581741, 28462984, 27881841)
Fulgent Genetics, Fulgent Genetics RCV002490770 SCV002795567 likely benign Autosomal recessive inherited pseudoxanthoma elasticum; Desbuquois dysplasia 2 2021-11-26 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001553443 SCV004699192 likely benign not provided 2024-01-01 criteria provided, single submitter clinical testing XYLT1: BP4, BS2
OMIM RCV000115037 SCV000148946 pathogenic Desbuquois dysplasia 2 2014-03-06 no assertion criteria provided literature only
Reproductive Health Research and Development, BGI Genomics RCV000115037 SCV001142462 uncertain significance Desbuquois dysplasia 2 2020-01-06 no assertion criteria provided curation NG_015843.1(NM_022166.3):c.1588-3C>T in XYLT1 gene has an allele frequency of 0.006 in Ashkenazi Jewish subpopulation in the gnomAD database. 3 homozygous occurrences are observed in the gnomAD database. This variant has been detected in an individual with Desbuquois dysplasia 2 (PMID: 24581741). Benign computational verdict because benign prediction from DANN. The available evidence is currently insufficient to determine the role of this variant in disease. We interpret it as variant of uncertain significance (VUS). ACMG/AMP criteria applied: PP3; PP4.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001553443 SCV001979852 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001553443 SCV001980463 likely benign not provided no assertion criteria provided clinical testing

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