ClinVar Miner

Submissions for variant NM_020702.5(MYORG):c.1967T>C (p.Ile656Thr)

gnomAD frequency: 0.00003  dbSNP: rs370944350
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
SIB Swiss Institute of Bioinformatics RCV000853524 SCV000996482 uncertain significance Basal ganglia calcification, idiopathic, 7, autosomal recessive 2019-06-13 criteria provided, single submitter curation This variant is interpreted as a variant of Uncertain significance for Basal ganglia calcification, idiopathic, 7, autosomal recessive. The following ACMG Tag(s) were applied: PM2, PP3.
Ambry Genetics RCV001266300 SCV001444473 uncertain significance Inborn genetic diseases 2019-12-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002536198 SCV003253575 pathogenic not provided 2024-04-20 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 656 of the KIAA1161 protein (p.Ile656Thr). This variant is present in population databases (rs370944350, gnomAD 0.01%). This missense change has been observed in individuals with primary basal ganglia calcification (PMID: 30649222, 31009047, 31951047, 32211515). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 692177). 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) performed at Invitae indicates that this missense variant is expected to disrupt KIAA1161 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

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