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NM_000289.6(PFKM):c.2087G>A (p.Arg696His) AND Glycogen storage disease, type VII

Germline classification:
Benign/Likely benign (5 submissions)
Last evaluated:
Jan 31, 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:
RCV000631186.24

Allele description [Variation Report for NM_000289.6(PFKM):c.2087G>A (p.Arg696His)]

NM_000289.6(PFKM):c.2087G>A (p.Arg696His)

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.2087G>A (p.Arg696His)
HGVS:
  • NC_000012.12:g.48145125G>A
  • NG_016199.2:g.44873G>A
  • NM_000289.6:c.2087G>AMANE SELECT
  • NM_001166686.2:c.2300G>A
  • NM_001166687.2:c.2087G>A
  • NM_001166688.2:c.2087G>A
  • NM_001354735.1:c.2396G>A
  • NM_001354736.1:c.2396G>A
  • NM_001354737.1:c.2300G>A
  • NM_001354738.1:c.2300G>A
  • NM_001354739.1:c.2300G>A
  • NM_001354740.1:c.2231G>A
  • NM_001354741.2:c.2111G>A
  • NM_001354742.2:c.2087G>A
  • NM_001354743.2:c.2087G>A
  • NM_001354744.2:c.2087G>A
  • NM_001354745.2:c.2000G>A
  • NM_001354746.2:c.1961G>A
  • NM_001354747.2:c.1937G>A
  • NM_001354748.2:c.1937G>A
  • NM_001363619.2:c.1994G>A
  • NP_000280.1:p.Arg696His
  • NP_001160158.1:p.Arg767His
  • NP_001160159.1:p.Arg696His
  • NP_001160160.1:p.Arg696His
  • NP_001341664.1:p.Arg799His
  • NP_001341665.1:p.Arg799His
  • NP_001341666.1:p.Arg767His
  • NP_001341667.1:p.Arg767His
  • NP_001341668.1:p.Arg767His
  • NP_001341669.1:p.Arg744His
  • NP_001341670.1:p.Arg704His
  • NP_001341671.1:p.Arg696His
  • NP_001341672.1:p.Arg696His
  • NP_001341673.1:p.Arg696His
  • NP_001341674.1:p.Arg667His
  • NP_001341675.1:p.Arg654His
  • NP_001341676.1:p.Arg646His
  • NP_001341677.1:p.Arg646His
  • NP_001350548.1:p.Arg665His
  • LRG_1177t1:c.2087G>A
  • LRG_1177:g.44873G>A
  • LRG_1177p1:p.Arg696His
  • NC_000012.11:g.48538908G>A
  • NM_000289.5:c.2087G>A
  • NM_001166686.1:c.2300G>A
  • NR_148954.2:n.2390G>A
  • NR_148955.1:n.3160G>A
  • NR_148956.2:n.2316G>A
  • NR_148957.2:n.2545G>A
  • NR_148958.2:n.2293G>A
  • NR_148959.2:n.2219G>A
  • P08237:p.Arg696His
Protein change:
R646H
Links:
UniProtKB: P08237#VAR_006069; dbSNP: rs41291971
NCBI 1000 Genomes Browser:
rs41291971
Molecular consequence:
  • NM_000289.6:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166686.2:c.2300G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166687.2:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001166688.2:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354735.1:c.2396G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354736.1:c.2396G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354737.1:c.2300G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354738.1:c.2300G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354739.1:c.2300G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354740.1:c.2231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354741.2:c.2111G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354742.2:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354743.2:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354744.2:c.2087G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354745.2:c.2000G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354746.2:c.1961G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354747.2:c.1937G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354748.2:c.1937G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363619.2:c.1994G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148954.2:n.2390G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148955.1:n.3160G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148956.2:n.2316G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148957.2:n.2545G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148958.2:n.2293G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148959.2:n.2219G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000752199Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Benign
(Jan 31, 2024)
germlineclinical testing

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

SCV000790129Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))
Likely benign
(Mar 6, 2017)
unknownclinical testing

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

Citation Link,

SCV000884300ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)
Benign
(Nov 2, 2023)
germlineclinical testing

Citation Link,

SCV001268751Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)
Likely benign
(Apr 27, 2017)
germlineclinical testing

Citation Link,

SCV001712287Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(May 18, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

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 (3)

Details of each submission

From Invitae, SCV000752199.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Counsyl, SCV000790129.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884300.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Illumina Laboratory Services, Illumina, SCV001268751.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV001712287.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 17, 2024