ClinVar Miner

Submissions for variant NM_014467.3(SRPX2):c.224A>T (p.Lys75Met)

gnomAD frequency: 0.00005  dbSNP: rs767072861
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000766861 SCV000243208 uncertain significance not provided 2013-05-01 criteria provided, single submitter clinical testing The Lys75Met missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 5,200 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The amino acid substitution is non-conservative as a positively charged, polar Lysine residue is replaced by an uncharged, non-polar Methionine residue. Lys75Met alters a position in the Sushi 1 domain that is conserved among positively charged amino acids in the SRPX2 protein and another missense mutation at a nearby codon (Tyr72Ser) has been reported in an individual with bilateral perisylvian polymicrogyria and Rolandic seizures (Roll et al., 2006). However, several in-silico algorithms predict Lys75Met may be non-pathogenic. Therefore, based on the currently available information, it is unclear whether Lys75Met is a disease-causing mutation or a rare benign variant. Mutations in the SRPX2 gene are inherited in an X-linked manner. Heterozygous females were reported to have a range of clinical phenotypes from no history of speech delay or epilepsy to severe oral-facial dyspraxia, intellectual disability, and Rolandic seizures (Roll et al., 2006). Mutations elsewhere in the evaluated gene would not be identified by this targeted analysis. The variant is found in EPILEPSY panel(s).
Eurofins Ntd Llc (ga) RCV000189565 SCV000856636 likely benign not specified 2017-09-20 criteria provided, single submitter clinical testing
Invitae RCV001078974 SCV001008191 likely benign Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked 2024-01-15 criteria provided, single submitter clinical testing

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