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NM_000289.6(PFKM):c.1063-6C>A AND Glycogen storage disease, type VII

Germline classification:
Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:
Jan 28, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV001286776.12

Allele description [Variation Report for NM_000289.6(PFKM):c.1063-6C>A]

NM_000289.6(PFKM):c.1063-6C>A

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.1063-6C>A
HGVS:
  • NC_000012.12:g.48139279C>A
  • NG_016199.2:g.39027C>A
  • NM_000289.6:c.1063-6C>AMANE SELECT
  • NM_001166686.2:c.1276-6C>A
  • NM_001166687.2:c.1063-6C>A
  • NM_001166688.2:c.1063-6C>A
  • NM_001354735.1:c.1372-6C>A
  • NM_001354736.1:c.1372-6C>A
  • NM_001354737.1:c.1276-6C>A
  • NM_001354738.1:c.1276-6C>A
  • NM_001354739.1:c.1276-6C>A
  • NM_001354740.1:c.1207-6C>A
  • NM_001354741.2:c.1087-6C>A
  • NM_001354742.2:c.1063-6C>A
  • NM_001354743.2:c.1063-6C>A
  • NM_001354744.2:c.1063-6C>A
  • NM_001354745.2:c.976-6C>A
  • NM_001354746.2:c.937-6C>A
  • NM_001354747.2:c.913-6C>A
  • NM_001354748.2:c.913-6C>A
  • NM_001363619.2:c.970-6C>A
  • LRG_1177t1:c.1063-6C>A
  • LRG_1177:g.39027C>A
  • NC_000012.11:g.48533062C>A
Links:
dbSNP: rs371033104
NCBI 1000 Genomes Browser:
rs371033104
Molecular consequence:
  • NM_000289.6:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001166686.2:c.1276-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001166687.2:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001166688.2:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354735.1:c.1372-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354736.1:c.1372-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354737.1:c.1276-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354738.1:c.1276-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354739.1:c.1276-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354740.1:c.1207-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354741.2:c.1087-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354742.2:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354743.2:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354744.2:c.1063-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354745.2:c.976-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354746.2:c.937-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354747.2:c.913-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354748.2:c.913-6C>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001363619.2:c.970-6C>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV001473393ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)
Uncertain significance
(Sep 18, 2019)
germlineclinical testing

Citation Link,

SCV002091076Natera, Inc.
no assertion criteria provided
Uncertain significance
(Feb 26, 2020)
germlineclinical testing

SCV003453063Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 28, 2024)
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

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

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV001473393.1

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

From Natera, Inc., SCV002091076.1

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

From Invitae, SCV003453063.2

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

Last Updated: Feb 28, 2024