NC_000015.9:g.(?_75189332)_(75190071_?)del AND MPI-congenital disorder of glycosylation

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 20, 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:: RCV004583037.1

Allele description

NC_000015.9:g.(?_75189332)_(75190071_?)del

Gene:: MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 15q24.1
Genomic location:: Chr15: 75189332 - 75190071 (on Assembly GRCh37)
Preferred name:: NC_000015.9:g.(?_75189332)_(75190071_?)del
HGVS:: NC_000015.9:g.(?_75189332)_(75190071_?)del
This HGVS expression did not pass validation

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005064111	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 20, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10484808, 30545931, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005064111

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 20, 2023)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Hyperinsulinemic hypoglycemia as a presenting sign in phosphomannose isomerase deficiency: A new manifestation of carbohydrate-deficient glycoprotein syndrome treatable with mannose.

de Lonlay P, Cuer M, Vuillaumier-Barrot S, Beaune G, Castelnau P, Kretz M, Durand G, Saudubray JM, Seta N.

J Pediatr. 1999 Sep;135(3):379-83.

PubMed [citation]

PMID:: 10484808

MPI-CDG with transient hypoglycosylation and antithrombin deficiency.

de la Morena-Barrio ME, Wypasek E, Owczarek D, Miñano A, Vicente V, Corral J, Undas A.

Haematologica. 2019 Feb;104(2):e79-e82. doi: 10.3324/haematol.2018.211326. Epub 2018 Dec 13. No abstract available.

PubMed [citation]

PMID:: 30545931
PMCID:: PMC6355499

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV005064111.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 7-8 of the MPI gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. This variant has not been reported in the literature in individuals affected with MPI-related conditions. This variant disrupts a region of the MPI protein in which other variant(s) (p.Ile398Thr) have been determined to be pathogenic (PMID: 10484808, 30545931). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 7, 2024

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