ClinVar Miner

Submissions for variant NM_005334.3(HCFC1):c.3892G>A (p.Glu1298Lys)

gnomAD frequency: 0.00007  dbSNP: rs781949446
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000522865 SCV000618700 uncertain significance not provided 2017-07-03 criteria provided, single submitter clinical testing The E1298K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The E1298K variant is observed in 1/9303 (0.01%) alleles from individuals of Latino background, including 1 hemizygous individual in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The E1298K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV001314423 SCV001504957 likely benign Methylmalonic acidemia with homocystinuria, type cblX 2024-02-19 criteria provided, single submitter clinical testing
Ambry Genetics RCV002527603 SCV003706879 uncertain significance Inborn genetic diseases 2022-04-12 criteria provided, single submitter clinical testing The c.3892G>A (p.E1298K) alteration is located in exon 17 (coding exon 17) of the HCFC1 gene. This alteration results from a G to A substitution at nucleotide position 3892, causing the glutamic acid (E) at amino acid position 1298 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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