NM_000289.6(PFKM):c.2047_2092+14del AND Glycogen storage disease, type VII

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 7, 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:: RCV003495402.3

Allele description [Variation Report for NM_000289.6(PFKM):c.2047_2092+14del]

NM_000289.6(PFKM):c.2047_2092+14del

Gene:

PFKM:phosphofructokinase, muscle [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_000289.6(PFKM):c.2047_2092+14del

HGVS:

NC_000012.12:g.48145085_48145144del
NG_016199.2:g.44833_44892del
NM_000289.6:c.2047_2092+14delMANE SELECT
NM_001166686.2:c.2260_2305+14del
NM_001166687.2:c.2047_2092+14del
NM_001166688.2:c.2047_2092+14del
NM_001354735.1:c.2356_2401+14del
NM_001354736.1:c.2356_2401+14del
NM_001354737.1:c.2260_2305+14del
NM_001354738.1:c.2260_2305+14del
NM_001354739.1:c.2260_2305+14del
NM_001354740.1:c.2191_2236+14del
NM_001354741.2:c.2071_2116+14del
NM_001354742.2:c.2047_2092+14del
NM_001354743.2:c.2047_2092+14del
NM_001354744.2:c.2047_2092+14del
NM_001354745.2:c.1960_2005+14del
NM_001354746.2:c.1921_1966+14del
NM_001354747.2:c.1897_1942+14del
NM_001354748.2:c.1897_1942+14del
NM_001363619.2:c.1954_1999+14del
LRG_1177t1:c.2047_2092+14del
LRG_1177:g.44833_44892del
NC_000012.11:g.48538866_48538925del
NC_000012.11:g.48538868_48538927del

Links:

dbSNP: rs2498677983

NCBI 1000 Genomes Browser:

rs2498677983

Molecular consequence:

NM_000289.6:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001166686.2:c.2260_2305+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001166687.2:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001166688.2:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354735.1:c.2356_2401+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354736.1:c.2356_2401+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354737.1:c.2260_2305+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354738.1:c.2260_2305+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354739.1:c.2260_2305+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354740.1:c.2191_2236+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354741.2:c.2071_2116+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354742.2:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354743.2:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354744.2:c.2047_2092+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354745.2:c.1960_2005+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354746.2:c.1921_1966+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354747.2:c.1897_1942+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354748.2:c.1897_1942+14del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001363619.2:c.1954_1999+14del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Glycogen storage disease, type VII (GSD7)
Synonyms:: GSD VII; MUSCLE PHOSPHOFRUCTOKINASE DEFICIENCY; PFKM DEFICIENCY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009295; MedGen: C0017926; Orphanet: 371; OMIM: 232800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004245333	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Nov 7, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 7825568, 8037209, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004245333

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Nov 7, 2023)

germline

clinical testing

PubMed (4)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency.

Raben N, Exelbert R, Spiegel R, Sherman JB, Nakajima H, Plotz P, Heinisch J.

Am J Hum Genet. 1995 Jan;56(1):131-41.

PubMed [citation]

PMID:: 7825568
PMCID:: PMC1801305

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004245333.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant results in the deletion of part of exon 21 (c.2047_2092+14del) of the PFKM gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PFKM are known to be pathogenic (PMID: 7825568, 8037209). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PFKM-related conditions. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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: May 16, 2025

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