ClinVar Miner

Submissions for variant NM_000359.3(TGM1):c.802del (p.Val268fs)

dbSNP: rs1322979131
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672184 SCV000797264 likely pathogenic Autosomal recessive congenital ichthyosis 1 2018-01-18 criteria provided, single submitter clinical testing
Invitae RCV001042112 SCV001205776 pathogenic not provided 2023-09-15 criteria provided, single submitter clinical testing This premature translational stop signal has been observed in individual(s) with congenital ichthyosis (PMID: 19241467). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 556211). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val268Phefs*62) in the TGM1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TGM1 are known to be pathogenic (PMID: 18948357, 19241467).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001844218 SCV002103461 pathogenic Lamellar ichthyosis 2022-02-26 criteria provided, single submitter clinical testing Variant summary: TGM1 c.802delG (p.Val268PhefsX62) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251428 control chromosomes. c.802delG has been reported in the literature as a compound heterozygous genotype with another pathogenic variant in the TGM1 gene inat-least one individual affected with Autosomal Recessive Congenital Ichthyosis (ARCI) (example, Herman_2009). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx RCV001042112 SCV002504089 pathogenic not provided 2022-02-14 criteria provided, single submitter clinical testing Frameshift 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; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 19241467)
Genome-Nilou Lab RCV000672184 SCV002763851 likely pathogenic Autosomal recessive congenital ichthyosis 1 criteria provided, single submitter clinical testing
Baylor Genetics RCV000672184 SCV004203804 pathogenic Autosomal recessive congenital ichthyosis 1 2023-11-26 criteria provided, single submitter clinical testing
Natera, Inc. RCV000672184 SCV002091226 pathogenic Autosomal recessive congenital ichthyosis 1 2020-09-22 no assertion criteria provided clinical testing

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