NM_000289.6(PFKM):c.1005A>G (p.Val335=) AND Glycogen storage disease, type VII

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Nov 24, 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:: RCV000686340.6

Allele description [Variation Report for NM_000289.6(PFKM):c.1005A>G (p.Val335=)]

NM_000289.6(PFKM):c.1005A>G (p.Val335=)

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.1005A>G (p.Val335=)

HGVS:

NC_000012.12:g.48137789A>G
NG_016199.2:g.37537A>G
NM_000289.6:c.1005A>GMANE SELECT
NM_001166686.2:c.1218A>G
NM_001166687.2:c.1005A>G
NM_001166688.2:c.1005A>G
NM_001354735.1:c.1314A>G
NM_001354736.1:c.1314A>G
NM_001354737.1:c.1218A>G
NM_001354738.1:c.1218A>G
NM_001354739.1:c.1218A>G
NM_001354740.1:c.1149A>G
NM_001354741.2:c.1029A>G
NM_001354742.2:c.1005A>G
NM_001354743.2:c.1005A>G
NM_001354744.2:c.1005A>G
NM_001354745.2:c.918A>G
NM_001354746.2:c.937-1496A>G
NM_001354747.2:c.855A>G
NM_001354748.2:c.855A>G
NM_001363619.2:c.912A>G
NP_000280.1:p.Val335=
NP_001160158.1:p.Val406=
NP_001160159.1:p.Val335=
NP_001160160.1:p.Val335=
NP_001341664.1:p.Val438=
NP_001341665.1:p.Val438=
NP_001341666.1:p.Val406=
NP_001341667.1:p.Val406=
NP_001341668.1:p.Val406=
NP_001341669.1:p.Val383=
NP_001341670.1:p.Val343=
NP_001341671.1:p.Val335=
NP_001341672.1:p.Val335=
NP_001341673.1:p.Val335=
NP_001341674.1:p.Val306=
NP_001341676.1:p.Val285=
NP_001341677.1:p.Val285=
NP_001350548.1:p.Val304=
LRG_1177t1:c.1005A>G
LRG_1177:g.37537A>G
LRG_1177p1:p.Val335=
NC_000012.11:g.48531572A>G
NM_000289.5:c.1005A>G
NR_148954.2:n.1308A>G
NR_148955.1:n.2078A>G
NR_148956.2:n.1234A>G
NR_148957.2:n.1308A>G
NR_148958.2:n.1056A>G
NR_148959.2:n.982A>G

Links:

dbSNP: rs1454843075

NCBI 1000 Genomes Browser:

rs1454843075

Molecular consequence:

NM_001354746.2:c.937-1496A>G - intron variant - [Sequence Ontology: SO:0001627]
NR_148954.2:n.1308A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148955.1:n.2078A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148956.2:n.1234A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148957.2:n.1308A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148958.2:n.1056A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148959.2:n.982A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000289.6:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001166686.2:c.1218A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001166687.2:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001166688.2:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354735.1:c.1314A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354736.1:c.1314A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354737.1:c.1218A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354738.1:c.1218A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354739.1:c.1218A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354740.1:c.1149A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354741.2:c.1029A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354742.2:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354743.2:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354744.2:c.1005A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354745.2:c.918A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354747.2:c.855A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354748.2:c.855A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363619.2:c.912A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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

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MULTISPECIES: toxin [Lysinibacillus]
MULTISPECIES: toxin [Lysinibacillus]
gi|501248773|ref|WP_012291791.1|

Protein
Homo sapiens TNF alpha induced protein 8 like 1 (TNFAIP8L1), transcript variant ...
Homo sapiens TNF alpha induced protein 8 like 1 (TNFAIP8L1), transcript variant 2, mRNA
gi|1519314858|ref|NM_152362.3|

Nucleotide
Homo sapiens ankyrin repeat domain 39 (ANKRD39), mRNA
Homo sapiens ankyrin repeat domain 39 (ANKRD39), mRNA
gi|1519311480|ref|NM_016466.6|

Nucleotide
Homo sapiens COMM domain containing 6 (COMMD6), transcript variant 2, mRNA
Homo sapiens COMM domain containing 6 (COMMD6), transcript variant 2, mRNA
gi|1890336106|ref|NM_203495.4|

Nucleotide
Cognitive Behavior Therapy - StatPearls
Cognitive Behavior Therapy - StatPearls

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000813856	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Nov 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002091075	Natera, Inc.	no assertion criteria provided	Uncertain significance (Sep 21, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000813856

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Nov 24, 2023)

germline

clinical testing

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

SCV002091075

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Sep 21, 2021)

germline

clinical testing

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000813856.3

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

#	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

From Natera, Inc., SCV002091075.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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: Sep 29, 2024

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