ClinVar Miner

Submissions for variant NM_000254.3(MTR):c.3600del (p.Ile1201fs)

dbSNP: rs1346847201
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000732987 SCV000860994 pathogenic not provided 2018-04-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003768229 SCV004651050 pathogenic Methylcobalamin deficiency type cblG 2023-12-26 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile1201Leufs*3) in the MTR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MTR are known to be pathogenic (PMID: 9683607, 12068375). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with MRT-related conditions (PMID: 34269512). ClinVar contains an entry for this variant (Variation ID: 596996). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003768229 SCV005203786 pathogenic Methylcobalamin deficiency type cblG 2024-07-02 criteria provided, single submitter clinical testing Variant summary: MTR c.3600delC (p.Ile1201LeufsX3) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 4e-06 in 251422 control chromosomes. c.3600delC has been reported in the literature as a compound heterozygous genotype in at-least one individual affected with isolated homocysteine re-methylation defect, a feature of Methylcobalamin deficiency type cblG (example, Whitehouse_2023). The following publication has been ascertained in the context of this evaluation (PMID: 37404677). ClinVar contains an entry for this variant (Variation ID: 596996). Based on the evidence outlined above, the variant was classified as pathogenic.

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