ClinVar Genomic variation as it relates to human health

Variant summary: The MPL c.305G>C (p.Arg102Pro) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 56/121606 control chromosomes at a frequency of 0.0004605, which does not exceed the estimated maximal expected allele frequency of a pathogenic MPL variant (0.002357). The variant was reported in numerous CAMPT patients in the literature, both in the homozygous and compound heterozygous state. Functional studies have shown the variant to lead to abnormal subcellular receptor distribution, lack of membrane localization, impaired glycosylation as well as impaired TPO signal transduction (Stockklausner_2015, Tijssen_2008). Taken together, this variant is classified as pathogenic.

MPL: PM3:Very Strong, PM2, PM5, PS3:Supporting

This sequence has been previously described in multiple patients with congenital amegakaryocytic thrombocytopenia (CAMT) in both homozygous and compound heterozygous states with other pathogenic variants in the same gene (PMIDs: 11972523, 28859041, 16470591, 18240171, 19302922, 21225925, 24119002, 26854587). Functional studies have shown that this sequence change impairs trafficking and glycosylation of the receptor expressed at the cell surface (PMIDs: 19302922, 24438083, 25538044). This sequence change has been described in the gnomAD database with a population frequency of 0.071% in non-Finnish Europeans; however, it has not been observed in homozygous state in any individuals (dbSNP rs28928907). The p.Arg102Pro change affects a highly conserved amino acid residue located in the extracellular domain of the MPL protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Arg102Pro substitution. These collective evidences indicate that this sequence change is pathogenic.

This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 102 of the MPL protein (p.Arg102Pro). This variant is present in population databases (rs28928907, gnomAD 0.07%). This missense change has been observed in individual(s) with congenital amegakaryocytic thrombocytopenia (CAMT) (PMID: 971406, 11972523, 16470591, 18240171, 19302922, 21225925, 24119002, 26854587, 28859041). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 14158). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MPL protein function. Experimental studies have shown that this missense change affects MPL function (PMID: 18422784, 19302922, 24438083, 25538044). This variant disrupts the p.Arg102 amino acid residue in MPL. Other variant(s) that disrupt this residue have been observed in individuals with MPL-related conditions (PMID: 16470591, 21659346), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.

Observed with a second MPL variant in additional patients with congenital amegakaryocytic thrombocytopenia in published literature, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes in some cases (PMID: 19302922, 32581362, 10971406); Identified in the heterozygous state in members of a single family with mild thrombocytosis and/or elevated thrombopoietin levels (PMID: 28979237); Published functional studies demonstrate a damaging effect due to impaired subcellular distribution, impaired glycosylation, and lack of JAK/STAT pathway activation (PMID: 25538044); In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24728327, 23351976, 27418648, 28034873, 32703794, 18422784, 16470591, 11133753, 15374889, 20188141, 26854587, 26556299, 28955303, 30431218, 30523342, 31589614, 37939832, 35776903, 32191290, 35150448, 34308104, 28859041, 24119002, 31064749, 32581362, 10971406, 19302922, 38752375, 37647632, 25538044, 28979237)

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with recessive congenital amegakaryocytic thrombocytopenia (CAMT) (MIM#604498) and dominant thrombocythemia 2 (MIM#601977), respectively (PMIDs: 28955303, 26423830). (I) 0108 - This gene is associated with autosomal dominant and recessive disease (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to proline. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (107 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v3) (9 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated ligand binding domain (PDB, NCBI). (I) 0703 - Another missense variant comparable to the one identified in this case has moderate previous evidence for pathogenicity. The p.(Arg102Cys) variant has been reported in multiple times, once as pathogenic in a patient with congenital amegakaryocytic thrombocytopenia (CAMT) (ClinVar) and several times in homozygous individuals with CAMT (PMIDs: 25539746, 21659346). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as pathogenic and observed in multiple individuals with autosomal recessive CAMT (ClinVar, PMIDs: 26854587, 21225925, 11972523). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. In vitro studies using transfected human cells showed MPL protein localisation and phosphorylation of signaling proteins were impaired (PMIDs: 28034873, 18422784). (SP) 1101 - Very strong and specific phenotype match for this individual. (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

PM1, PM3_strong, PM5, PS3, PS4