ClinVar Miner

Submissions for variant NM_001558.4(IL10RA):c.506T>C (p.Ile169Thr)

gnomAD frequency: 0.00004  dbSNP: rs369219156
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001214188 SCV001385859 likely pathogenic Inflammatory bowel disease 28 2023-03-03 criteria provided, single submitter clinical testing Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on IL10RA protein function. ClinVar contains an entry for this variant (Variation ID: 943905). This missense change has been observed in individual(s) with early onset inflammatory bowel disease (PMID: 22549091, 24813381; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs369219156, gnomAD 0.004%). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 169 of the IL10RA protein (p.Ile169Thr). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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