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NM_002435.3(MPI):c.65del (p.Gly22fs) AND MPI-congenital disorder of glycosylation

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 29, 2023
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:
RCV003516093.2

Allele description [Variation Report for NM_002435.3(MPI):c.65del (p.Gly22fs)]

NM_002435.3(MPI):c.65del (p.Gly22fs)

Gene:
MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q24.1
Genomic location:
Preferred name:
NM_002435.3(MPI):c.65del (p.Gly22fs)
HGVS:
  • NC_000015.10:g.74890575del
  • NG_008921.1:g.5507del
  • NG_008921.2:g.5535del
  • NG_131687.1:g.718del
  • NG_131687.2:g.807del
  • NM_001289155.2:c.65del
  • NM_001289156.2:c.-7+486del
  • NM_001289157.2:c.65del
  • NM_001330372.2:c.5del
  • NM_002435.3:c.65delMANE SELECT
  • NP_001276084.1:p.Gly22fs
  • NP_001276086.1:p.Gly22fs
  • NP_001317301.1:p.Gly2fs
  • NP_002426.1:p.Gly22fs
  • NC_000015.9:g.75182914del
  • NC_000015.9:g.75182916del
Protein change:
G22fs
Molecular consequence:
  • NM_001289155.2:c.65del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289157.2:c.65del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330372.2:c.5del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002435.3:c.65del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330372.2:c.5del - initiator_codon_variant - [Sequence Ontology: SO:0001582]
  • NM_001289156.2:c.-7+486del - intron variant - [Sequence Ontology: SO:0001627]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004335506Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 29, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Congenital disorders of glycosylation: an update on defects affecting the biosynthesis of dolichol-linked oligosaccharides.

Haeuptle MA, Hennet T.

Hum Mutat. 2009 Dec;30(12):1628-41. doi: 10.1002/humu.21126. Review.

PubMed [citation]
PMID:
19862844

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004335506.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Gly22Valfs*50) in the MPI gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MPI are known to be pathogenic (PMID: 19862844). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MPI-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024