NM_000303.3(PMM2):c.264_265del (p.His90fs) AND PMM2-congenital disorder of glycosylation

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 15, 2020
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:: RCV001389071.5

Allele description [Variation Report for NM_000303.3(PMM2):c.264_265del (p.His90fs)]

NM_000303.3(PMM2):c.264_265del (p.His90fs)

Gene:

PMM2:phosphomannomutase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p13.2

Genomic location:

Preferred name:

NM_000303.3(PMM2):c.264_265del (p.His90fs)

HGVS:

NC_000016.10:g.8806324_8806325del
NG_009209.1:g.13512_13513del
NM_000303.3:c.264_265delMANE SELECT
NP_000294.1:p.His90fs
NC_000016.9:g.8900180_8900181del
NC_000016.9:g.8900181_8900182del

Protein change:

H90fs

Links:

dbSNP: rs2141019983

NCBI 1000 Genomes Browser:

rs2141019983

Molecular consequence:

NM_000303.3:c.264_265del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Saccharomyces cerevisiae S288C Aim24p (AIM24), partial mRNA
Saccharomyces cerevisiae S288C Aim24p (AIM24), partial mRNA
gi|296146086|ref|NM_001181738.1|

Nucleotide
dai20e10.x1 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4959859 3' similar to...
dai20e10.x1 NICHD_XGC_Emb4 Xenopus laevis cDNA clone IMAGE:4959859 3' similar to SW:VATD_BOVIN P39942 VACUOLAR ATP SYNTHASE SUBUNIT D, mRNA sequence
gi|17923425|gnl|dbEST|10653478|gb|B 85.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001590276	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 15, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 19862844, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001590276

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 15, 2020)

germline

clinical testing

PubMed (2)
[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

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, SCV001590276.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.His90Serfs*3) in the PMM2 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 not been reported in the literature in individuals with PMM2-related conditions. Loss-of-function variants in PMM2 are known to be pathogenic (PMID: 19862844). 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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