ClinVar Miner

Submissions for variant NM_000092.5(COL4A4):c.4082-1G>T

dbSNP: rs1559438651
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000681810 SCV001400674 likely pathogenic not provided 2023-11-30 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 42 of the COL4A4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COL4A4 are known to be pathogenic (PMID: 21196518, 24854265, 25307543). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with Alport syndrome and/or COL4A4-related conditions (PMID: 30586318; Invitae). ClinVar contains an entry for this variant (Variation ID: 562353). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV003233810 SCV003932199 likely pathogenic Benign familial hematuria 2023-01-13 criteria provided, single submitter clinical testing PVS1_Moderate, PM1, PM2, PM3_Supporting
Gharavi Laboratory, Columbia University RCV000681810 SCV000809281 pathogenic not provided 2018-09-16 no assertion criteria provided research

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