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NM_000289.6(PFKM):c.299G>A (p.Arg100Gln)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Jul 12, 2021)
Last evaluated:
Jul 1, 2021
Accession:
VCV000255760.7
Variation ID:
255760
Description:
single nucleotide variant
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NM_000289.6(PFKM):c.299G>A (p.Arg100Gln)

Allele ID
254569
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
12q13.11
Genomic location
12: 48132929 (GRCh38) GRCh38 UCSC
12: 48526712 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000012.11:g.48526712G>A
NC_000012.12:g.48132929G>A
NM_000289.6:c.299G>A MANE Select NP_000280.1:p.Arg100Gln missense
... more HGVS
Protein change
R100Q, R171Q, R50Q, R108Q, R148Q, R203Q, R71Q
Other names
NM_000289.5(PFKM):c.299G>A(p.Arg100Gln)
NM_001166686.1(PFKM):c.512G>A(p.Arg171Gln)
NM_001166687.1(PFKM):c.299G>A(p.Arg100Gln)
NM_001166688.1(PFKM):c.299G>A(p.Arg100Gln)
Canonical SPDI
NC_000012.12:48132928:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.14776 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.17225
Exome Aggregation Consortium (ExAC) 0.17778
The Genome Aggregation Database (gnomAD) 0.15760
1000 Genomes Project 0.14776
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.17192
The Genome Aggregation Database (gnomAD), exomes 0.17814
Links
ClinGen: CA6536961
UniProtKB: P08237#VAR_006065
dbSNP: rs2228500
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 3 criteria provided, multiple submitters, no conflicts Jan 8, 2016 RCV000245226.3
Benign 6 criteria provided, multiple submitters, no conflicts Jul 1, 2021 RCV000322166.7
Benign 1 no assertion criteria provided Dec 16, 2015 RCV000675434.2
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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
324 337

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000303490.1
Submitted: (Apr 28, 2016)
Evidence details
Benign
(Jan 08, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000517627.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(May 31, 2018)
criteria provided, single submitter
Method: curation
Glycogen storage disease, type VII
Allele origin: unknown
SIB Swiss Institute of Bioinformatics
Accession: SCV000803447.1
Submitted: (Jun 13, 2018)
Evidence details
Comment:
This variant is interpreted as a Benign - Stand Alone, for Glycogen storage disease VII, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: … (more)
Benign
(Jul 17, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000332947.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Mar 06, 2018)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000379093.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Aug 31, 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: SCV000604622.4
Submitted: (Dec 11, 2020)
Evidence details
Benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Invitae
Accession: SCV001719754.1
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jul 01, 2021)
criteria provided, single submitter
Method: clinical testing
Glycogen storage disease, type VII
Allele origin: germline
Pars Genome Lab
Accession: SCV001750026.1
Submitted: (Jul 12, 2021)
Evidence details
Benign
(Dec 16, 2015)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000801114.1
Submitted: (May 23, 2018)
Evidence details
Benign
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Glycogen storage disease type VII
Allele origin: germline
Natera, Inc.
Accession: SCV001457679.1
Submitted: (Dec 28, 2020)
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PFKM - - - -

Text-mined citations for rs2228500...

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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 Jul 14, 2021