Submissions for variant NM_004092.4(ECHS1):c.541C>T (p.Arg181Cys)

gnomAD frequency: 0.00001  dbSNP: rs754609693

Total submissions: 1

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000578160	SCV000680014	likely pathogenic	Mitochondrial short-chain Enoyl-Coa hydratase 1 deficiency	2017-05-05	criteria provided, single submitter	clinical testing	The NM_004092.3(ECHS1):c.541C>T missense variant is in exon 5 of the ECHS1 gene (chr10:135180471). This substitution is predicted to create a change of an arginine to a cysteine at amino acid position 181, NP_004083.3(ECHS1):p.(Arg181Cys), which is considered significant. The arginine at this position has high conservation and therefore Grantham assessment (A-GVGD) is likely pathogenic. In silico software predicts this variant to be disease causing. It is situated within a known functional region (conserved trimeric quaternary structure which contains the catalytic core). This variant has not been previously observed in our patient cohort and has not been previously reported, but it has been observed in a population database at a frequency of 0.001% (ExAC). The variant is present in trans with a likely pathogenic ECHS1 variant, and additional biochemical evaluation is consistent with ECHS1 deficiency. Based on current information and biochemical evidence, this variant has been classified as LIKELY PATHOGENIC.