NM_000303.3(PMM2):c.17_28del (p.Pro6_Cys9del) AND PMM2-congenital disorder of glycosylation

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 4, 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:: RCV002890998.3

Allele description [Variation Report for NM_000303.3(PMM2):c.17_28del (p.Pro6_Cys9del)]

NM_000303.3(PMM2):c.17_28del (p.Pro6_Cys9del)

Gene:

PMM2:phosphomannomutase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_000303.3(PMM2):c.17_28del (p.Pro6_Cys9del)

HGVS:

NC_000016.10:g.8797899_8797910del
NG_009209.1:g.5087_5098del
NG_033146.1:g.4742_4753del
NG_133047.1:g.767_778del
NG_133048.1:g.72_83del
NM_000303.3:c.17_28delMANE SELECT
NP_000294.1:p.Pro6_Cys9del
NC_000016.9:g.8891753_8891764del
NC_000016.9:g.8891756_8891767del

Molecular consequence:

NM_000303.3:c.17_28del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: PMM2-congenital disorder of glycosylation
Synonyms:: CDG Ia; CARBOHYDRATE-DEFICIENT GLYCOPROTEIN SYNDROME, TYPE Ia; CDG 1A; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008907; MedGen: C0349653; Orphanet: 79318; OMIM: 212065

Recent activity

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Mus musculus solute carrier family 22 (organic cation transporter), member 5 (Sl...
Mus musculus solute carrier family 22 (organic cation transporter), member 5 (Slc22a5), transcript variant 3, mRNA
gi|2621013443|ref|NM_001362712.2|

Nucleotide
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Coregonus maraena partial mRNA for six transmembrane epithelial antigen of prostate (STEAP4 gene)
gi|662488834|emb|LK054751.1|

Nucleotide
Coregonus maraena partial mRNA for TLR8a2 protein (TLR8a2 gene)
Coregonus maraena partial mRNA for TLR8a2 protein (TLR8a2 gene)
gi|930189584|emb|LN876657.1|

Nucleotide
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003247680	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 4, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10922383, 11715002, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003247680

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 4, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of four novel PMM2 mutations in congenital disorders of glycosylation (CDG) Ia French patients.

Vuillaumier-Barrot S, Hetet G, Barnier A, Dupré T, Cuer M, de Lonlay P, Cormier-Daire V, Durand G, Grandchamp B, Seta N.

J Med Genet. 2000 Aug;37(8):579-80.

PubMed [citation]

PMID:: 10922383
PMCID:: PMC1734666

Functional significance of PMM2 mutations in mildly affected patients with congenital disorders of glycosylation Ia.

Westphal V, Peterson S, Patterson M, Tournay A, Blumenthal A, Treacy EP, Freeze HH.

Genet Med. 2001 Nov-Dec;3(6):393-8.

PubMed [citation]

PMID:: 11715002

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003247680.2

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

Description

This variant disrupts a region of the PMM2 protein in which other variant(s) (p.Cys9Tyr) have been determined to be pathogenic (PMID: 10922383, 11715002). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with PMM2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.1%). This variant, c.17_28del, results in the deletion of 4 amino acid(s) of the PMM2 protein (p.Pro6_Cys9del), but otherwise preserves the integrity of the reading frame. 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	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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