ClinVar Miner

Submissions for variant NM_000213.5(ITGB4):c.1666C>T (p.Arg556Cys)

gnomAD frequency: 0.00038  dbSNP: rs150166497
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000301781 SCV000406536 uncertain significance Junctional epidermolysis bullosa with pyloric atresia 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV001764294 SCV001989446 uncertain significance not provided 2022-02-08 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001764294 SCV003248718 likely benign not provided 2024-01-24 criteria provided, single submitter clinical testing
Ambry Genetics RCV004021713 SCV004888523 uncertain significance Inborn genetic diseases 2023-11-03 criteria provided, single submitter clinical testing The c.1666C>T (p.R556C) alteration is located in coding exon 13 of the ITGB4 gene. This alteration results from a C to T substitution at nucleotide position 1666, causing the arginine (R) at amino acid position 556 to be replaced by a cysteine (C). Based on data from gnomAD, the T allele has an overall frequency of 0.032% (90/282480) total alleles studied. The highest observed frequency was 0.064% (82/128992) of European (non-Finnish) alleles. This amino acid position is not well conserved in available vertebrate species. The in silico prediction for this alteration is inconclusive. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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