ClinVar Miner

Submissions for variant NM_000213.5(ITGB4):c.599C>T (p.Pro200Leu)

dbSNP: rs148770294
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001355966 SCV002451800 likely benign not provided 2024-01-27 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355966 SCV001551002 uncertain significance not provided no assertion criteria provided clinical testing The ITGB4 p.Pro200Leu variant was identified in 1 of 8 patients with epidermolysis bullosa as a compound heterozygous variant and in 1 of 13 patients with phenotypes suggestive of Fine-Lubinsky syndrome with the variant inherited from the unaffected father (Schumann_2013_PMID:23496044; Niceta_2015_PMID:25865493). The variant was identified in dbSNP (ID: rs148770294) but was not identified in ClinVar. The variant was identified in control databases in 232 of 282838 chromosomes at a frequency of 0.0008203 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (Finnish) in 73 of 25122 chromosomes (freq: 0.002906), European (non-Finnish) in 123 of 129160 chromosomes (freq: 0.000952), Latino in 26 of 35432 chromosomes (freq: 0.000734), Other in 5 of 7224 chromosomes (freq: 0.000692), African in 4 of 24960 chromosomes (freq: 0.00016) and South Asian in 1 of 30616 chromosomes (freq: 0.000033), but was not observed in the Ashkenazi Jewish or East Asian populations. The p.Pro200 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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