NM_002435.3(MPI):c.843_844+1del AND MPI-congenital disorder of glycosylation

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 16, 2022
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:: RCV002805808.3

Allele description [Variation Report for NM_002435.3(MPI):c.843_844+1del]

NM_002435.3(MPI):c.843_844+1del

Gene:

MPI:mannose phosphate isomerase [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

15q24.1

Genomic location:

Preferred name:

NM_002435.3(MPI):c.843_844+1del

HGVS:

NC_000015.10:g.74896321AGG[1]
NG_008921.1:g.11253AGG[1]
NG_008921.2:g.11281AGG[1]
NM_001289155.2:c.843_844+1del
NM_001289156.2:c.693_694+1del
NM_001289157.2:c.660_661+1del
NM_001330372.2:c.783_784+1del
NM_002435.3:c.843_844+1delMANE SELECT
NC_000015.9:g.75188662AGG[1]
NC_000015.9:g.75188662_75188664del

Molecular consequence:

NM_001289155.2:c.843_844+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001289156.2:c.693_694+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001289157.2:c.660_661+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001330372.2:c.783_784+1del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_002435.3:c.843_844+1del - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV003029708	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003029708

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 16, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003029708.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with MPI-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This variant, c.842_844del, results in the deletion of 1 amino acid(s) of the MPI protein (p.Gly281del), but otherwise preserves the integrity of the reading frame.

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

Last Updated: Sep 29, 2024

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