NM_000289.6(PFKM):c.1426A>T (p.Lys476Ter) AND Glycogen storage disease, type VII

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 19, 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:: RCV003496212.1

Allele description

NM_000289.6(PFKM):c.1426A>T (p.Lys476Ter)

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.1426A>T (p.Lys476Ter)

HGVS:

NC_000012.12:g.48141753A>T
NG_016199.2:g.41501A>T
NM_000289.6:c.1426A>TMANE SELECT
NM_001166686.2:c.1639A>T
NM_001166687.2:c.1426A>T
NM_001166688.2:c.1426A>T
NM_001354735.1:c.1735A>T
NM_001354736.1:c.1735A>T
NM_001354737.1:c.1639A>T
NM_001354738.1:c.1639A>T
NM_001354739.1:c.1639A>T
NM_001354740.1:c.1570A>T
NM_001354741.2:c.1450A>T
NM_001354742.2:c.1426A>T
NM_001354743.2:c.1426A>T
NM_001354744.2:c.1426A>T
NM_001354745.2:c.1339A>T
NM_001354746.2:c.1300A>T
NM_001354747.2:c.1276A>T
NM_001354748.2:c.1276A>T
NM_001363619.2:c.1333A>T
NP_000280.1:p.Lys476Ter
NP_001160158.1:p.Lys547Ter
NP_001160159.1:p.Lys476Ter
NP_001160160.1:p.Lys476Ter
NP_001341664.1:p.Lys579Ter
NP_001341665.1:p.Lys579Ter
NP_001341666.1:p.Lys547Ter
NP_001341667.1:p.Lys547Ter
NP_001341668.1:p.Lys547Ter
NP_001341669.1:p.Lys524Ter
NP_001341670.1:p.Lys484Ter
NP_001341671.1:p.Lys476Ter
NP_001341672.1:p.Lys476Ter
NP_001341673.1:p.Lys476Ter
NP_001341674.1:p.Lys447Ter
NP_001341675.1:p.Lys434Ter
NP_001341676.1:p.Lys426Ter
NP_001341677.1:p.Lys426Ter
NP_001350548.1:p.Lys445Ter
LRG_1177t1:c.1426A>T
LRG_1177:g.41501A>T
LRG_1177p1:p.Lys476Ter
NC_000012.11:g.48535536A>T
NR_148954.2:n.1729A>T
NR_148955.1:n.2499A>T
NR_148956.2:n.1655A>T
NR_148957.2:n.1884A>T
NR_148958.2:n.1632A>T
NR_148959.2:n.1558A>T

Protein change:

K426*

Molecular consequence:

NR_148954.2:n.1729A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148955.1:n.2499A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148956.2:n.1655A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148957.2:n.1884A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148958.2:n.1632A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148959.2:n.1558A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000289.6:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166686.2:c.1639A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166687.2:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001166688.2:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354735.1:c.1735A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354736.1:c.1735A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354737.1:c.1639A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354738.1:c.1639A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354739.1:c.1639A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354740.1:c.1570A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354741.2:c.1450A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354742.2:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354743.2:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354744.2:c.1426A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354745.2:c.1339A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354746.2:c.1300A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354747.2:c.1276A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001354748.2:c.1276A>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363619.2:c.1333A>T - 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

Recent activity

Clear Turn Off Turn On

Graecoanatolica vegorriticola isolate GraVeg_Veg_5 cytochrome oxidase subunit I ...
Graecoanatolica vegorriticola isolate GraVeg_Veg_5 cytochrome oxidase subunit I (COX1) gene, partial cds; mitochondrial
gi|564282252|gb|KF758779.1|

Nucleotide
Chain B, Protein transport protein SEC13
Chain B, Protein transport protein SEC13
gi|151567862|pdb|2PM6|B

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004364277	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 19, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 7825568, 8037209, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004364277

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 19, 2023)

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

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 (3)

Details of each submission

From Invitae, SCV004364277.1

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

Description

This sequence change creates a premature translational stop signal (p.Lys476*) 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). This variant has not been reported in the literature in individuals affected with PFKM-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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: Feb 20, 2024

ClinVar

Relating variation to medicine