ClinVar Genomic variation as it relates to human health
NM_000289.6(PFKM):c.31dup (p.Thr11fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000289.6(PFKM):c.31dup (p.Thr11fs)
Variation ID: 1725563 Accession: VCV001725563.2
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 12q13.11 12: 48122801-48122802 (GRCh38) [ NCBI UCSC ] 12: 48516584-48516585 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 19, 2022 Dec 24, 2022 Mar 30, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000289.6:c.31dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000280.1:p.Thr11fs frameshift NM_001166686.2:c.244dup NP_001160158.1:p.Thr82fs frameshift NM_001166687.2:c.31dup NP_001160159.1:p.Thr11fs frameshift NM_001166688.2:c.31dup NP_001160160.1:p.Thr11fs frameshift NM_001354735.1:c.340dup NP_001341664.1:p.Thr114fs frameshift NM_001354736.1:c.340dup NP_001341665.1:p.Thr114fs frameshift NM_001354737.1:c.244dup NP_001341666.1:p.Thr82fs frameshift NM_001354738.1:c.244dup NP_001341667.1:p.Thr82fs frameshift NM_001354739.1:c.244dup NP_001341668.1:p.Thr82fs frameshift NM_001354740.1:c.175dup NP_001341669.1:p.Thr59fs frameshift NM_001354741.2:c.55dup NP_001341670.1:p.Thr19fs frameshift NM_001354742.2:c.31dup NP_001341671.1:p.Thr11fs frameshift NM_001354743.2:c.31dup NP_001341672.1:p.Thr11fs frameshift NM_001354744.2:c.31dup NP_001341673.1:p.Thr11fs frameshift NM_001354745.2:c.-295dup 5 prime UTR NM_001354746.2:c.31dup NP_001341675.1:p.Thr11fs frameshift NM_001354747.2:c.-46dup 5 prime UTR NM_001354748.2:c.-46dup 5 prime UTR NM_001363619.2:c.31dup NP_001350548.1:p.Thr11fs frameshift NR_148954.2:n.82dup non-coding transcript variant NR_148955.1:n.614dup non-coding transcript variant NR_148956.2:n.82dup non-coding transcript variant NR_148957.2:n.82dup non-coding transcript variant NR_148958.2:n.82dup non-coding transcript variant NR_148959.2:n.82dup non-coding transcript variant NC_000012.12:g.48122805dup NC_000012.11:g.48516588dup NG_016199.2:g.22553dup LRG_1177:g.22553dup LRG_1177t1:c.31dup LRG_1177p1:p.Thr11fs - Protein change
- T114fs, T11fs, T19fs, T59fs, T82fs
- Other names
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- Canonical SPDI
- NC_000012.12:48122801:AAAA:AAAAA
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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PFKM | - | - |
GRCh38 GRCh37 |
916 | 933 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Likely pathogenic (1) |
criteria provided, single submitter
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Mar 30, 2022 | RCV002309247.2 |
Submissions - Germline
Classification
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The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Mar 30, 2022)
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criteria provided, single submitter
Method: clinical testing
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Glycogen storage disease, type VII
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV002603057.2
First in ClinVar: Nov 19, 2022 Last updated: Dec 24, 2022 |
Comment:
NM_001166686.1(PFKM):c.244dupA(T82Nfs*43) is expected to be pathogenic in the context of glycogen storage disease type VII. This variant is predicted to lead to an abnormal or … (more)
NM_001166686.1(PFKM):c.244dupA(T82Nfs*43) is expected to be pathogenic in the context of glycogen storage disease type VII. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in PFKM, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening. (less)
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Germline Functional Evidence
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 germline classification of this variant
HelpThere are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for this variant ...
HelpRecord last updated Dec 24, 2022
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.