NM_000289.6(PFKM):c.1607del (p.Gly535_Ser536insTer) AND Glycogen storage disease, type VII

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Jan 25, 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:: RCV001380454.7

Allele description [Variation Report for NM_000289.6(PFKM):c.1607del (p.Gly535_Ser536insTer)]

NM_000289.6(PFKM):c.1607del (p.Gly535_Ser536insTer)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_000289.6(PFKM):c.1607del (p.Gly535_Ser536insTer)

HGVS:

NC_000012.12:g.48142020del
NG_016199.2:g.41768del
NM_000289.6:c.1607delMANE SELECT
NM_001166686.2:c.1820del
NM_001166687.2:c.1607del
NM_001166688.2:c.1607del
NM_001354735.1:c.1916del
NM_001354736.1:c.1916del
NM_001354737.1:c.1820del
NM_001354738.1:c.1820del
NM_001354739.1:c.1820del
NM_001354740.1:c.1751del
NM_001354741.2:c.1631del
NM_001354742.2:c.1607del
NM_001354743.2:c.1607del
NM_001354744.2:c.1607del
NM_001354745.2:c.1520del
NM_001354746.2:c.1481del
NM_001354747.2:c.1457del
NM_001354748.2:c.1457del
NM_001363619.2:c.1514del
NP_000280.1:p.Gly535_Ser536insTer
NP_001160158.1:p.Gly606_Ser607insTer
NP_001160159.1:p.Gly535_Ser536insTer
NP_001160160.1:p.Gly535_Ser536insTer
NP_001341664.1:p.Gly638_Ser639insTer
NP_001341665.1:p.Gly638_Ser639insTer
NP_001341666.1:p.Gly606_Ser607insTer
NP_001341667.1:p.Gly606_Ser607insTer
NP_001341668.1:p.Gly606_Ser607insTer
NP_001341669.1:p.Gly583_Ser584insTer
NP_001341670.1:p.Gly543_Ser544insTer
NP_001341671.1:p.Gly535_Ser536insTer
NP_001341672.1:p.Gly535_Ser536insTer
NP_001341673.1:p.Gly535_Ser536insTer
NP_001341674.1:p.Gly506_Ser507insTer
NP_001341675.1:p.Gly493_Ser494insTer
NP_001341676.1:p.Gly485_Ser486insTer
NP_001341677.1:p.Gly485_Ser486insTer
NP_001350548.1:p.Gly504_Ser505insTer
LRG_1177t1:c.1607del
LRG_1177:g.41768del
LRG_1177p1:p.Gly535_Ser536insTer
NC_000012.11:g.48535803del
NR_148954.2:n.1910del
NR_148955.1:n.2680del
NR_148956.2:n.1836del
NR_148957.2:n.2065del
NR_148958.2:n.1813del
NR_148959.2:n.1739del

Links:

dbSNP: rs866260025

NCBI 1000 Genomes Browser:

rs866260025

Molecular consequence:

NR_148954.2:n.1910del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148955.1:n.2680del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148956.2:n.1836del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148957.2:n.2065del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148958.2:n.1813del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148959.2:n.1739del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000289.6:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001166686.2:c.1820del - nonsense - [Sequence Ontology: SO:0001587]
NM_001166687.2:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001166688.2:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354735.1:c.1916del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354736.1:c.1916del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354737.1:c.1820del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354738.1:c.1820del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354739.1:c.1820del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354740.1:c.1751del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354741.2:c.1631del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354742.2:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354743.2:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354744.2:c.1607del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354745.2:c.1520del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354746.2:c.1481del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354747.2:c.1457del - nonsense - [Sequence Ontology: SO:0001587]
NM_001354748.2:c.1457del - nonsense - [Sequence Ontology: SO:0001587]
NM_001363619.2:c.1514del - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Glycogen storage disease, type VII (GSD7)
Synonyms:: GSD VII; Glycogen storage disease type 7; Muscle phosphofructokinase 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
SCV001578536	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 3, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7825568, 8037209, 28492532
SCV004203930	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 25, 2024)	unknown	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

SCV001578536

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 3, 2022)

germline

clinical testing

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

SCV004203930

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 25, 2024)

unknown

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, SCV001578536.4

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1068782). This variant has not been reported in the literature in individuals affected with PFKM-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser536*) 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).

#	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, SCV004203930.2

#	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

Last Updated: Sep 29, 2024

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