ClinVar Miner

Submissions for variant NM_001001547.3(CD36):c.1228_1239del (p.Ile410_Ile413del) (rs550565800)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000490260 SCV000267243 likely pathogenic Platelet glycoprotein IV deficiency 2016-03-18 criteria provided, single submitter reference population
Illumina Clinical Services Laboratory,Illumina RCV000490260 SCV000916211 pathogenic Platelet glycoprotein IV deficiency 2018-01-04 criteria provided, single submitter clinical testing The CD36 c.1228_1239delATTGTGCCTATT (p. Ile410_Ile413del) variant, also referred to as c. 1438_1449del, has been reported in five studies in a total of 13 individuals with platelet glycoprotein IV deficiency, including three in a homozygous state, four in a compound heterozygous state, and six in a heterozygous state (Kashiwagi et al. 2001; Tanaka et al. 2001; Li et al. 2014; Masuda et al. 2015; Lo et al. 2016). Typically, individuals homozygous or compound heterozygous for the p.Ile410_Ile413del variant show a type I phenotype with CD36 deficiency on the surface of both platelets and monocytes, while some individuals heterozygous for the variant show a type II phenotype with CD36 deficiency only on the surface of platelets. The p.Ile410_Ile413del variant was found in two unaffected parents of an affected individual and 15/192 control individuals (Kashiwagi et al. 2001; Tanaka et al. 2001; Masuda et al. 2015) in a heterozygous state and is reported at a frequency of 0.01119 in the East Asian population of the Genome Aggregation Database. The 15 control individuals who were heterozygous for the variant had low CD36 expression, but not low enough to be classified as type II. Absence of CD36 surface expression on platelets and monocytes of patient samples was shown by flow cytometry (Kashiwagi et al. 2001; Tanaka et al. 2001; Li et al. 2014; Masuda et al. 2015; Lo et al. 2016). In addition, immunofluorescence experiments with c.1228_1239del expression in HEK293T cells revealed the CD36 protein was retained in the cytoplasm (Kashiwagi et al. 2001). Based on the collective evidence, the p.Ile410_Ile413del variant is classified as pathogenic for platelet glycoprotein IV deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
Reproductive Health Research and Development,BGI Genomics RCV000490260 SCV001142373 likely pathogenic Platelet glycoprotein IV deficiency 2020-01-06 no assertion criteria provided curation NM_001001547.2:c.1228_1239delATTGTGCCTATT in the CD36 gene has an allele frequency of 0.011 in East Asian subpopulation in the gnomAD database. The CD36 c.1228_1239delATTGTGCCTATT (p. Ile410_Ile413del) variant, also referred to as c. 1438_1449del, has been reported in multiple individuals with platelet glycoprotein IV deficiency, including in homozygous state (PMID: 26528880) and compound heterozygous state with 329-330del (PMID: 25330908). Immunofluorescence experiments with c.1228_1239del expression in HEK293T cells revealed the CD36 protein was retained in the cytoplasm (PMID: 11499670). Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP Criteria applied: PM3; PM4; PS3; PP4.

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