ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.1931_1932inv (p.Thr644Met)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000174597 SCV000225919 benign not specified 2014-09-16 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590030 SCV000699475 benign not provided 2017-04-27 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.1931_1932delinsTG (p.Thr644delinsMet) variant involves the alteration a dinucleotide, resulting in a missense substitution that is not within a known functional domain (InterPro). 2/2 in silico tool predicts a damaging outcome for this variant (SNPs&GO was excluded due to a low reliability index and PolyPhen was unavailable during this analysis). This variant was found in 1646/122718 control chromosomes (24 homozygotes) at a frequency of 0.0134129, which is approximately 6 times the estimated maximal expected allele frequency of a pathogenic GNPTAB variant (0.0022361), suggesting this variant is likely a benign polymorphism. One clinical diagnostic laboratory has classified this variant as benign. In contrast, functional assays have suggested that protein function was partially impaired by the variant, which was identified in a mucolipidosis III patient in compound heterozygote state (Velho_2015, the other variant: c.3668_3670delCTA/T1223del). However, the patial loss of protein activity of GNPTAB-T644M in HEK-293 cells may not present in vivo or not be significant enough to cause disease. Taken together, this variant is classified as benign.
Invitae RCV001079779 SCV001107509 likely benign Mucolipidosis type II; Pseudo-Hurler polydystrophy 2019-12-31 criteria provided, single submitter clinical testing

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