ClinVar Miner

Submissions for variant NM_001079802.2(FKTN):c.607C>T (p.Arg203Ter)

gnomAD frequency: 0.00001  dbSNP: rs746763506
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center RCV000490403 SCV000267316 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4; Autosomal recessive limb-girdle muscular dystrophy type 2M; Muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4 2016-03-18 criteria provided, single submitter reference population
Invitae RCV000234557 SCV000285819 pathogenic Walker-Warburg congenital muscular dystrophy 2023-11-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg203*) in the FKTN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FKTN are known to be pathogenic (PMID: 17044012, 17878207, 18752264). This variant is present in population databases (rs746763506, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with FKTN-related disease (PMID: 11165248, 20961758, 26809617). ClinVar contains an entry for this variant (Variation ID: 225359). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000255310 SCV000322218 pathogenic not provided 2020-06-22 criteria provided, single submitter clinical testing Reported in ClinVar as a pathogenic variant (ClinVar Variant ID# 225359; Landrum et al., 2016); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 20961758, 25525159, 11165248, 26809617, 28688748, 14627679)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590733 SCV000698717 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 2016-05-06 criteria provided, single submitter clinical testing Variant summary: The FKTN variant, c.607C>T (p.Arg203X) causes a nonsense mutation in exon 5 resulting in a premature termination codon, a known mechanism for disease, as these types of variants are predicted to cause transcript degradation through nonsense mediated decay or produce a truncated protein. The varinat of interest was observed in the large, broad control population, ExAC, with an allele frequency of 1/121290, which does not exceed the estimated maximum expected allele frequency for a pathogenic FKTN variant of 1/200 for Fukuyama Congenital Muscular Dystrophy. The variant of interest has been reported in multiple affected individuals dx with Fukuyama Congenital Muscular Dystrophy (patient was homozygous for variant) and Muscular dystrophy-dystroglycanopathy(limb-girdle) via publications. One reputable database cites the variant as disease-causing. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Pathogenic.
Counsyl RCV000590733 SCV000790450 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 2017-03-21 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002503833 SCV002797302 pathogenic Dilated cardiomyopathy 1X; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4; Autosomal recessive limb-girdle muscular dystrophy type 2M; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1; Muscular dystrophy-dystroglycanopathy (congenital without intellectual disability), type B4 2022-04-01 criteria provided, single submitter clinical testing
Baylor Genetics RCV001594387 SCV004199739 pathogenic Dilated cardiomyopathy 1X 2023-05-11 criteria provided, single submitter clinical testing
KTest Genetics, KTest RCV001594387 SCV001499958 pathogenic Dilated cardiomyopathy 1X no assertion criteria provided clinical testing

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