NM_002435.3(MPI):c.166dup (p.Arg56fs) AND MPI-CDG

Clinical significance:Pathogenic/Likely pathogenic (Last evaluated: Jun 26, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000169342.4

Allele description [Variation Report for NM_002435.3(MPI):c.166dup (p.Arg56fs)]

NM_002435.3(MPI):c.166dup (p.Arg56fs)

Gene:
MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
15q24.1
Genomic location:
Preferred name:
NM_002435.3(MPI):c.166dup (p.Arg56fs)
HGVS:
  • NC_000015.10:g.74891400dup
  • NG_008921.1:g.6332dup
  • NM_001289155.2:c.166dup
  • NM_001289156.2:c.16dup
  • NM_001289157.2:c.166dup
  • NM_001330372.2:c.106dup
  • NM_002435.3:c.166dupMANE SELECT
  • NP_001276084.1:p.Arg56fs
  • NP_001276085.1:p.Arg6fs
  • NP_001276086.1:p.Arg56fs
  • NP_001317301.1:p.Arg36fs
  • NP_002426.1:p.Arg56fs
  • NC_000015.9:g.75183736_75183737insC
  • NC_000015.9:g.75183741dup
  • NM_002435.1:c.166dupC
Protein change:
R36fs
Links:
dbSNP: rs786204593
NCBI 1000 Genomes Browser:
rs786204593
Molecular consequence:
  • NM_001289155.2:c.166dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289156.2:c.16dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001289157.2:c.166dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001330372.2:c.106dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_002435.3:c.166dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
MPI-CDG
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
SCV000220704Counsylcriteria provided, single submitter
Likely pathogenic
(Sep 17, 2014)
unknownliterature only

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

Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015),

Citation Link,

SCV000938225Invitaecriteria provided, single submitter
Pathogenic
(Jun 26, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib).

Schollen E, Dorland L, de Koning TJ, Van Diggelen OP, Huijmans JG, Marquardt T, Babovic-Vuksanovic D, Patterson M, Imtiaz F, Winchester B, Adamowicz M, Pronicka E, Freeze H, Matthijs G.

Hum Mutat. 2000 Sep;16(3):247-52. Review.

PubMed [citation]
PMID:
10980531

[Congenital disorder of glycosylation type 1b. Experience with mannose treatment].

Martín Hernández E, Vega Pajares AI, Pérez González B, Ecay Crespo MJ, Leal Pérez F, Manzanares López-Manzanares J, Ugarte Pérez M, Pérez-Cerdá Silvestre C.

An Pediatr (Barc). 2008 Oct;69(4):358-65. Spanish.

PubMed [citation]
PMID:
18928705
See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000220704.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000938225.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Arg56Profs*8) in the MPI gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with congenital disorders of glycosylation type Ib (PMID: 10980531, 18928705). ClinVar contains an entry for this variant (Variation ID: 188967). Loss-of-function variants in MPI are known to be pathogenic (PMID: 19862844). 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: May 10, 2021

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