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NM_002435.3(MPI):c.414G>A (p.Met138Ile) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 22, 2017
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_002435.3(MPI):c.414G>A (p.Met138Ile)]

NM_002435.3(MPI):c.414G>A (p.Met138Ile)

MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_002435.3(MPI):c.414G>A (p.Met138Ile)
  • NC_000015.10:g.74892729G>A
  • NG_008921.1:g.7661G>A
  • NM_001289155.2:c.414G>A
  • NM_001289156.2:c.264G>A
  • NM_001289157.2:c.414G>A
  • NM_001330372.2:c.354G>A
  • NM_002435.3:c.414G>AMANE SELECT
  • NP_001276084.1:p.Met138Ile
  • NP_001276085.1:p.Met88Ile
  • NP_001276086.1:p.Met138Ile
  • NP_001317301.1:p.Met118Ile
  • NP_002426.1:p.Met138Ile
  • NC_000015.9:g.75185070G>A
  • NM_002435.1:c.414G>A
  • NM_002435.2:c.414G>A
Protein change:
dbSNP: rs150217523
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001289155.2:c.414G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289156.2:c.264G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001289157.2:c.414G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330372.2:c.354G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002435.3:c.414G>A - missense variant - [Sequence Ontology: SO:0001583]


none provided
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Jun 22, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000617147.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


The M138I variant in the MPI gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. This variant is observed in 66/10,400 alleles (0.63%) from individuals of African background in the ExAC dataset (Lek et al., 2016). The M138I variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In addition, this substitution occurs at a position where amino acids with similar properties to Methionine are tolerated across species, and Isoleucine is present in three mammalian species. However, in silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in the same codon (M138T) and a nearby residue (I140T) have been reported in the Human Gene Mutation Database in association with CDG1B (Jaeken et al., 1998; Stenson et al., 2014), supporting the functional importance of this region of the protein. We therefore interpret M138I as a variant of uncertain significance.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024