NM_001354735.1:c.12C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001354735.1(PFKM):c.12C>T(p.Asp4Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,596,808 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000073 ( 1 hom. )
Consequence
PFKM
NM_001354735.1 synonymous
NM_001354735.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0130
Publications
0 publications found
Genes affected
PFKM (HGNC:8877): (phosphofructokinase, muscle) Three phosphofructokinase isozymes exist in humans: muscle, liver and platelet. These isozymes function as subunits of the mammalian tetramer phosphofructokinase, which catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-bisphosphate. Tetramer composition varies depending on tissue type. This gene encodes the muscle-type isozyme. Mutations in this gene have been associated with glycogen storage disease type VII, also known as Tarui disease. Alternatively spliced transcript variants have been described.[provided by RefSeq, Nov 2009]
PFKM Gene-Disease associations (from GenCC):
- glycogen storage disease VIIInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, PanelApp Australia, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 12-48107385-C-T is Benign according to our data. Variant chr12-48107385-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2428748.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.013 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PFKM | NM_001354735.1 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 26 | NP_001341664.1 | ||
PFKM | NM_001354736.1 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 26 | NP_001341665.1 | ||
PFKM | NM_001166686.2 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 25 | NP_001160158.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PFKM | ENST00000642730.1 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 26 | ENSP00000496597.1 | ||||
PFKM | ENST00000340802.12 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 25 | 2 | ENSP00000345771.6 | |||
PFKM | ENST00000549366.5 | c.12C>T | p.Asp4Asp | synonymous_variant | Exon 2 of 7 | 4 | ENSP00000449622.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
152110
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.0000256 AC: 6AN: 234250 AF XY: 0.00000780 show subpopulations
GnomAD2 exomes
AF:
AC:
6
AN:
234250
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
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Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000727 AC: 105AN: 1444698Hom.: 1 Cov.: 29 AF XY: 0.0000751 AC XY: 54AN XY: 719340 show subpopulations
GnomAD4 exome
AF:
AC:
105
AN:
1444698
Hom.:
Cov.:
29
AF XY:
AC XY:
54
AN XY:
719340
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33434
American (AMR)
AF:
AC:
0
AN:
44710
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26118
East Asian (EAS)
AF:
AC:
1
AN:
39676
South Asian (SAS)
AF:
AC:
1
AN:
86202
European-Finnish (FIN)
AF:
AC:
0
AN:
39122
Middle Eastern (MID)
AF:
AC:
0
AN:
5758
European-Non Finnish (NFE)
AF:
AC:
102
AN:
1109484
Other (OTH)
AF:
AC:
0
AN:
60194
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.462
Heterozygous variant carriers
0
5
10
16
21
26
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74302 show subpopulations
GnomAD4 genome
AF:
AC:
3
AN:
152110
Hom.:
Cov.:
32
AF XY:
AC XY:
1
AN XY:
74302
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41414
American (AMR)
AF:
AC:
0
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4824
European-Finnish (FIN)
AF:
AC:
0
AN:
10596
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
2
AN:
68034
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.408
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disease, type VII Benign:1
Nov 23, 2022
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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