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

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Jul 20, 2021)
Last evaluated:
May 18, 2021
Accession:
VCV000255756.8
Variation ID:
255756
Description:
single nucleotide variant
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NM_000289.6(PFKM):c.2087G>A (p.Arg696His)

Allele ID
254585
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 48145125 (GRCh38) GRCh38 UCSC
12: 48538908 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48538908G>A
NC_000012.12:g.48145125G>A
NM_000289.6:c.2087G>A MANE Select NP_000280.1:p.Arg696His missense
... more HGVS
Protein change
R696H, R767H, R667H, R654H, R744H, R799H, R665H, R704H, R646H
Other names
-
Canonical SPDI
NC_000012.12:48145124:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00379 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00969
Trans-Omics for Precision Medicine (TOPMed) 0.01045
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01215
The Genome Aggregation Database (gnomAD) 0.01165
The Genome Aggregation Database (gnomAD), exomes 0.00969
1000 Genomes Project 0.00379
Links
ClinGen: CA6537526
UniProtKB: P08237#VAR_006069
dbSNP: rs41291971
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Jan 3, 2018 RCV000251357.4
Benign 2 criteria provided, single submitter Mar 24, 2021 RCV000675441.5
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations May 18, 2021 RCV000631186.7
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PFKM - - GRCh38
GRCh37
323 336

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303486.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Mar 06, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: unknown
Counsyl
Accession: SCV000790129.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Likely benign
(Jan 03, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000858857.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Aug 25, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV000884300.3
Submitted: (Dec 11, 2020)
Evidence details
Likely benign
(May 18, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001712287.1
Submitted: (Jun 08, 2021)
Evidence details
Benign
(Dec 04, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Invitae
Accession: SCV000752199.4
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 24, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000518805.5
Submitted: (Jul 20, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 22133655, 7825568, 22995991, 20981092)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001268751.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
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, … (more)
Likely benign
(Jan 09, 2018)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801121.1
Submitted: (May 23, 2018)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency. Raben N American journal of human genetics 1995 PMID: 7825568
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PFKM - - - -

Text-mined citations for rs41291971...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Aug 17, 2021