ClinVar Miner

Submissions for variant NM_024747.6(HPS6):c.2029G>A (p.Glu677Lys)

gnomAD frequency: 0.00006  dbSNP: rs373272114
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001103579 SCV001260356 likely benign Hermansky-Pudlak syndrome 6 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV001759870 SCV001987310 uncertain significance not provided 2019-09-24 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001759870 SCV002395060 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002555013 SCV003633439 uncertain significance Inborn genetic diseases 2021-07-09 criteria provided, single submitter clinical testing The c.2029G>A (p.E677K) alteration is located in exon 1 (coding exon 1) of the HPS6 gene. This alteration results from a G to A substitution at nucleotide position 2029, causing the glutamic acid (E) at amino acid position 677 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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