ClinVar Miner

Submissions for variant NM_001195263.2(PDZD7):c.2089del (p.Ala697fs)

dbSNP: rs1055318738
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota RCV001171317 SCV001334047 likely pathogenic Hearing loss, autosomal recessive 57 2020-02-18 criteria provided, single submitter clinical testing
GeneDx RCV001664724 SCV001875166 pathogenic not provided 2023-07-11 criteria provided, single submitter clinical testing Observed phase unknown with a second PDZD7 variant in unrelated patients with bilateral congenital sensorineural hearing loss referred for genetic testing at GeneDx; 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; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 20440071)
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV001171317 SCV002061713 likely pathogenic Hearing loss, autosomal recessive 57 2021-04-01 criteria provided, single submitter clinical testing PVS1, PM2
Invitae RCV001664724 SCV002129985 pathogenic not provided 2023-12-30 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ala697Profs*26) in the PDZD7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PDZD7 are known to be pathogenic (PMID: 20440071). This variant is present in population databases (no rsID available, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with PDZD7-related conditions. ClinVar contains an entry for this variant (Variation ID: 915843). For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics RCV002559641 SCV003686419 pathogenic Inborn genetic diseases 2020-04-07 criteria provided, single submitter clinical testing The c.2089delG (p.A697Pfs*26) alteration, located in exon 15 (coding exon 14) of the PDZD7 gene, consists of a deletion of one nucleotide at position 2089, causing a translational frameshift with a predicted alternate stop codon after 26 amino acids. Frameshift alterations are typically deleterious in nature (Richards, 2015). The alteration is rare in population databases: Based on data from the Genome Aggregation Database (gnomAD), the c.2089delG alteration was observed in 0.027% (44/162436) of total alleles studied, with a frequency of 0.17% (44/25210) in the Latino subpopulation. Based on the available evidence, this alteration is classified as pathogenic.

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