ClinVar Miner

Submissions for variant NM_000133.4(F9):c.-35G>A

gnomAD frequency: 0.00001  dbSNP: rs1166164399
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000795083 SCV000934525 pathogenic Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor 9 defect 2019-06-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has been reported to affect F9 protein function (PMID: 23472758, 2352926). This variant has been observed to segregate with hemophilia B Leyden in families (PMID: 7677806, 2352926) and has been observed in several unrelated affected individuals (PMID: 28168417, 2352926, 8251390, 10595634, 7734378, 8217825). This variant is also known as -6G>A in the literature. ClinVar contains an entry for this variant (Variation ID: 10559). This variant is not present in population databases (ExAC no frequency). This variant occurs in a non-coding region of the F9 gene. It does not change the encoded amino acid sequence of the F9 protein.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004586929 SCV005076562 pathogenic Hereditary factor IX deficiency disease 2024-04-24 criteria provided, single submitter clinical testing Variant summary: F9 c.-35G>A is located in the untranscribed region upstream of the F9 gene region. The variant was absent in 182805 control chromosomes. c.-35G>A (also known as -6G>A) has been reported in the literature in multiple individuals affected with hemophilia B Leydenin and segregated with disease in at least one family (e.g. Coyle_1994, Ahmed_2020, Hirosawa_1990, Tamura_2021). These data indicate that the variant is very likely to be associated with disease. Experimental studies show that this variant reduce the expression level of factor IX (Hirosawa_1990, Funnell_2013). The following publications have been ascertained in the context of this evaluation (PMID: 32346856, 7677806, 23472758, 2352926, 33427373). ClinVar contains an entry for this variant (Variation ID: 641767). Based on the evidence outlined above, the variant was classified as pathogenic.
OMIM RCV001815011 SCV000031533 pathogenic Hemophilia B leyden 1990-08-11 no assertion criteria provided literature only

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