ClinVar Miner

Submissions for variant NM_001291303.3(FAT4):c.9964G>A (p.Val3322Met)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clinical Genomics Laboratory, Washington University in St. Louis RCV004560375 SCV005047059 uncertain significance Hennekam lymphangiectasia-lymphedema syndrome 2 2024-01-11 criteria provided, single submitter clinical testing The FAT4 c.9964G>A (p.Val3322Met) variant was identified at a near heterozygous allele fraction of 49%, a frequency which may be consistent with it being of germline origin. Computational predictors are conflicting as to the impact of this variant on FAT4 function. This variant is only observed on 30/1,614,194 alleles in the general population (gnomAD v4.0.0), indicating it is not a common variant. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), the clinical significance of the FAT4 c.9964G>A (p.Val3322Met) variant is uncertain at this time.
Fulgent Genetics, Fulgent Genetics RCV005038712 SCV005657526 uncertain significance Van Maldergem syndrome 2; Hennekam lymphangiectasia-lymphedema syndrome 2 2024-04-16 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005059531 SCV005727048 uncertain significance not specified 2024-11-06 criteria provided, single submitter clinical testing Variant summary: FAT4 c.9958G>A (p.Val3320Met) results in a conservative amino acid change located in the Cadherin domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251016 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.9958G>A in individuals affected with FAT4-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 3237383). Based on the evidence outlined above, the variant was classified as uncertain significance.

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