ClinVar Miner

Submissions for variant NM_006412.4(AGPAT2):c.492+1G>A

gnomAD frequency: 0.00003  dbSNP: rs933422777
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV002274023 SCV002559460 likely pathogenic not provided 2022-02-08 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 20301391, 32041611, 14557463)
Neuberg Centre For Genomic Medicine, NCGM RCV000412609 SCV004048518 pathogenic Congenital generalized lipodystrophy type 1 criteria provided, single submitter clinical testing The variant is reported with the allele frequency of 0.001615% in gnomAD and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar as Pathogenic. The variant affects an invariant splice nucleotide and is expected to cause loss of function. Downstream loss of function variants have been reported to be disease causing. The nucleotide change in AGPAT2 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.
GeneReviews RCV000412609 SCV000490118 not provided Congenital generalized lipodystrophy type 1 no assertion provided literature only

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