ClinVar Miner

Submissions for variant NM_016030.6(TRAPPC12):c.361G>A (p.Glu121Lys)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002472123 SCV002768542 uncertain significance Early-onset progressive encephalopathy-hearing loss-pons hypoplasia-brain atrophy syndrome 2019-08-28 criteria provided, single submitter clinical testing A heterozygous missense variant was identified, NM_016030.5(TRAPPC12):c.361G>A in exon 2 of 12 of the TRAPPC12 gene. This substitution is predicted to create a minor amino acid change from glutamic acid to lysine at position 121 of the protein, NP_057114.5(TRAPPC12):p.(Glu121Lys). The glutamic acid at this position is only present, but also conserved, in mammals (100 vertebrates, UCSC), but is not situated in a known functional domain. In silico software predicts this variant to be benign (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD population database at a frequency of 0.13% (132 heterozygotes, 1 homozygote). The variant has not been previously reported in a clinical testing setting. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) with LOW CLINICAL RELEVANCE.
Labcorp Genetics (formerly Invitae), Labcorp RCV003669323 SCV004391303 benign not provided 2024-11-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV004067597 SCV004971936 likely benign Inborn genetic diseases 2024-01-09 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003896205 SCV004718699 benign TRAPPC12-related disorder 2019-09-11 no assertion criteria provided clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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