ClinVar Miner

Submissions for variant NM_001558.4(IL10RA):c.537G>A (p.Thr179=)

gnomAD frequency: 0.00001  dbSNP: rs1419560997
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Molecular Medicine, Children’s Hospital of Fudan University RCV001030031 SCV001190549 pathogenic Inflammatory bowel disease 28 2019-05-10 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001030031 SCV001378746 pathogenic Inflammatory bowel disease 28 2024-02-08 criteria provided, single submitter clinical testing This sequence change affects codon 179 of the IL10RA mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the IL10RA protein. This variant also falls at the last nucleotide of exon 4, which is part of the consensus splice site for this exon. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has been observed in individual(s) with Inflammatory bowel disease (PMID: 26822028, 28267044, 29140941). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 830051). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital RCV001030031 SCV001739465 likely pathogenic Inflammatory bowel disease 28 2020-02-28 criteria provided, single submitter clinical testing
Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine RCV001030031 SCV003837567 pathogenic Inflammatory bowel disease 28 2023-01-03 criteria provided, single submitter clinical testing
Aleixo Muise Laboratory, Hospital For Sick Children RCV001030031 SCV005088141 pathogenic Inflammatory bowel disease 28 2024-07-05 criteria provided, single submitter research PVS1;PS1;PM2;PP3;PP4

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