ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.6308A>G (p.Lys2103Arg)

gnomAD frequency: 0.00002  dbSNP: rs796053322
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189524 SCV000243167 uncertain significance not provided 2012-10-31 criteria provided, single submitter clinical testing p.Lys2103Arg (AAA>AGA):c.6308 A>G in exon 49 of the SPTAN1 gene (NM_001130438.1) The Lys2103Arg missense change has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The NHLBI ESP Exome Variant Project has not identified Lys2013Arg in approximately 6,500 individuals of European or African American ethnicity, indicating that it is not a common benign variant in these populations. This amino acid substitution is conservative, as both Arginine and Lysine are positively charged amino acids. Lys2103Arg alters a highly conserved position in the 22nd spectrin repeat of the protein, and multiple in silico algorithms predict it may be damaging to protein structure/function. However, previously reported pathogenic mutations in SPTAN1 are in frame deletions or duplications located within the last spectrin repeat of the protein (Saitsu et al., 2010). Therefore, based on the currently available information, it is unclear whether Lys2103Arg is a disease-causing mutation or a rare benign variant. The variant is found in EPILEPSY panel(s).
Labcorp Genetics (formerly Invitae), Labcorp RCV001089073 SCV000633791 likely benign Early infantile epileptic encephalopathy with suppression bursts 2024-01-07 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001808519 SCV002056582 uncertain significance Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV004668837 SCV005172986 uncertain significance Inborn genetic diseases 2024-05-12 criteria provided, single submitter clinical testing The c.6308A>G (p.K2103R) alteration is located in exon 49 (coding exon 48) of the SPTAN1 gene. This alteration results from a A to G substitution at nucleotide position 6308, causing the lysine (K) at amino acid position 2103 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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