NM_000289.6(PFKM):c.1807C>T (p.Arg603Ter) AND Glycogen storage disease, type VII

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Jan 3, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV002633476.6

Allele description [Variation Report for NM_000289.6(PFKM):c.1807C>T (p.Arg603Ter)]

NM_000289.6(PFKM):c.1807C>T (p.Arg603Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_000289.6(PFKM):c.1807C>T (p.Arg603Ter)

HGVS:

NC_000012.12:g.48142935C>T
NG_016199.2:g.42683C>T
NG_125592.1:g.605C>T
NM_000289.6:c.1807C>TMANE SELECT
NM_001166686.2:c.2020C>T
NM_001166687.2:c.1807C>T
NM_001166688.2:c.1807C>T
NM_001354735.1:c.2116C>T
NM_001354736.1:c.2116C>T
NM_001354737.1:c.2020C>T
NM_001354738.1:c.2020C>T
NM_001354739.1:c.2020C>T
NM_001354740.1:c.1951C>T
NM_001354741.2:c.1831C>T
NM_001354742.2:c.1807C>T
NM_001354743.2:c.1807C>T
NM_001354744.2:c.1807C>T
NM_001354745.2:c.1720C>T
NM_001354746.2:c.1681C>T
NM_001354747.2:c.1657C>T
NM_001354748.2:c.1657C>T
NM_001363619.2:c.1714C>T
NP_000280.1:p.Arg603Ter
NP_001160158.1:p.Arg674Ter
NP_001160159.1:p.Arg603Ter
NP_001160160.1:p.Arg603Ter
NP_001341664.1:p.Arg706Ter
NP_001341665.1:p.Arg706Ter
NP_001341666.1:p.Arg674Ter
NP_001341667.1:p.Arg674Ter
NP_001341668.1:p.Arg674Ter
NP_001341669.1:p.Arg651Ter
NP_001341670.1:p.Arg611Ter
NP_001341671.1:p.Arg603Ter
NP_001341672.1:p.Arg603Ter
NP_001341673.1:p.Arg603Ter
NP_001341674.1:p.Arg574Ter
NP_001341675.1:p.Arg561Ter
NP_001341676.1:p.Arg553Ter
NP_001341677.1:p.Arg553Ter
NP_001350548.1:p.Arg572Ter
LRG_1177t1:c.1807C>T
LRG_1177:g.42683C>T
LRG_1177p1:p.Arg603Ter
NC_000012.11:g.48536718C>T
NR_148954.2:n.2110C>T
NR_148955.1:n.2880C>T
NR_148956.2:n.2036C>T
NR_148957.2:n.2265C>T
NR_148958.2:n.2013C>T
NR_148959.2:n.1939C>T

Protein change:

R553*

Links:

dbSNP: rs1392144132

NCBI 1000 Genomes Browser:

rs1392144132

Molecular consequence:

NR_148954.2:n.2110C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148955.1:n.2880C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148956.2:n.2036C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148957.2:n.2265C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148958.2:n.2013C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148959.2:n.1939C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000289.6:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166686.2:c.2020C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166687.2:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166688.2:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354735.1:c.2116C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354736.1:c.2116C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354737.1:c.2020C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354738.1:c.2020C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354739.1:c.2020C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354740.1:c.1951C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354741.2:c.1831C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354742.2:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354743.2:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354744.2:c.1807C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354745.2:c.1720C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354746.2:c.1681C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354747.2:c.1657C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354748.2:c.1657C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363619.2:c.1714C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV003515120	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 15, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7825568, 8037209, 28492532
SCV004203950	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 7, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005634642	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 3, 2024)	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

SCV003515120

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 15, 2023)

germline

clinical testing

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

SCV004203950

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 7, 2023)

unknown

clinical testing

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

SCV005634642

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 3, 2024)

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

Citations

PubMed

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

Common mutations in the phosphofructokinase-M gene in Ashkenazi Jewish patients with glycogenesis VII--and their population frequency.

Sherman JB, Raben N, Nicastri C, Argov Z, Nakajima H, Adams EM, Eng CM, Cowan TM, Plotz PH.

Am J Hum Genet. 1994 Aug;55(2):305-13.

PubMed [citation]

PMID:: 8037209
PMCID:: PMC1918380

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003515120.3

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

Description

This variant has not been reported in the literature in individuals affected with PFKM-related conditions. This sequence change creates a premature translational stop signal (p.Arg603*) in the PFKM gene. It is expected to result in an absent or disrupted protein product. 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). ClinVar contains an entry for this variant (Variation ID: 2196187). 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

From Baylor Genetics, SCV004203950.1

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

#	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

From Fulgent Genetics, Fulgent Genetics, SCV005634642.1

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

#	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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