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

Clinical significance:Uncertain significance (Last evaluated: Jun 22, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000523642.3

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

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

Gene:
MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q24.1
Genomic location:
Preferred name:
NM_002435.3(MPI):c.414G>A (p.Met138Ile)
HGVS:
  • 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:
M118I
Links:
dbSNP: rs150217523
NCBI 1000 Genomes Browser:
rs150217523
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]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000617147GeneDxcriteria provided, single submitter
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

Description

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.

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

Last Updated: May 16, 2021

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