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NM_002435.3(MPI):c.414G>A (p.Met138Ile) AND MPI-congenital disorder of glycosylation

Germline classification:
Likely benign (2 submissions)
Last evaluated:
Jan 31, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001083362.9

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)

Name:
MPI-congenital disorder of glycosylation
Synonyms:
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE Ib; CDG Ib; Congenital disorder of glycosylation type 1B; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011257; MedGen: C1865145; Orphanet: 79319; OMIM: 602579

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001005085Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 31, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001454926Natera, Inc.
no assertion criteria provided
Benign
(Oct 28, 2019)
germlineclinical testing

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001005085.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001454926.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024