ClinVar Miner

Submissions for variant NM_000530.8(MPZ):c.116A>C (p.His39Pro) (rs371856018)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000206430 SCV000261054 pathogenic Charcot-Marie-Tooth disease, type I 2020-01-03 criteria provided, single submitter clinical testing This sequence change replaces histidine with proline at codon 39 of the MPZ protein (p.His39Pro). The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and proline. This variant is also known as p.His10Pro in the literature. This variant is not present in population databases (rs371856018, ExAC no frequency). This variant has been reported in multiple patients affected with Charcot-Marie-Tooth disease (CMT) (PMID: 14711881, 16844954, 26310628). In addition, it was found to segregate with CMT in two families (PMID: 16844954, 17602703). ClinVar contains an entry for this variant (Variation ID: 217232). Experimental studies have shown that this missense change leads to a decrease in MPZ-mediated intercellular adhesion in transfected cells (PMID: 18337304). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV000236108 SCV000292950 pathogenic not provided 2018-08-01 criteria provided, single submitter clinical testing The H39P pathogenic variant in the MPZ gene has been reported previously (using alternative nomenclature of H10P) in multiple unrelated individuals with late-onset neuropathy (CMT1B) (Shy et al., 2004; Souayah et al., 2007). It was also identified in a family of 10 individuals with hereditary motor and sensory neuropathy, and absent in 200 control individuals (Kilfoyle et al., 2006). Functional studies suggest that H39P may result in partial loss of function (Grandis et al., 2008). The H39P variant was not observed in large population cohorts (Lek et al, 2016). Additionally, many other missense variants in nearby residues have also been reported in the Human Gene Mutation Database in association with MPZ-related neuropathies (Stenson et al., 2014), supporting the functional importance of this region of the protein. Therefore, H39P is interpreted to be a pathogenic variant and its presence is consistent with the diagnosis of an MPZ-related disorder in this individual.
Athena Diagnostics Inc RCV000236108 SCV000614099 pathogenic not provided 2018-12-10 criteria provided, single submitter clinical testing Not found in the total gnomAD dataset, and the data is high quality. Found in at least one patient with expected phenotype for this gene. Located in potentially critical domain of the protein. This variant occurs as the most likely explanation for disease in a significant number of internal cases, suggesting this variant is associated with disease. Assessment of experimental evidence regarding the effect of this variant on protein function is inconclusive. Statistically associated with disease in multiple families.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001002484 SCV001160435 pathogenic not specified 2019-04-19 criteria provided, single submitter clinical testing The MPZ c.116A>C; p.His39Pro variant (rs371856018) is reported in the literature in numerous individuals affected with Charcot-Marie-Tooth syndrome or neuropathy (Kilfoyle 2006, Sanmaneechai 2015, Shy 2004, Souayah 2007). This variant was observed to co-segregate with disease in multiple families (Kilfoyle 2006, Shy 2004, Souayah 2007), including one large family where it was observed in 10 affected individuals and was absent from 24 unaffected individuals (Kilfoyle 2006). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Based on available information, including its occurrence in a large number of affected individuals, this variant is considered to be pathogenic. References: Kilfoyle DH et al. Myelin protein zero mutation His39Pro: hereditary motor and sensory neuropathy with variable onset, hearing loss, restless legs and multiple sclerosis. J Neurol Neurosurg Psychiatry. 2006 Aug;77(8):963-6. Sanmaneechai O et al. Genotype-phenotype characteristics and baseline natural history of heritable neuropathies caused by mutations in the MPZ gene. Brain. 2015 Nov;138(Pt 11):3180-92. Shy ME et al. Phenotypic clustering in MPZ mutations. Brain. 2004 Feb;127(Pt 2):371-84. Souayah N et al. Rare myelin protein zero sequence variant in late onset CMT1B. J Neurol Sci. 2007 Dec 15;263(1-2):177-9.

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