ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.244_250del (p.Phe82fs)
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_000038.6(APC):c.244_250del (p.Phe82fs)
Variation ID: 2092032 Accession: VCV002092032.2
- Type and length
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Deletion, 7 bp
- Location
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Cytogenetic: 5q22.2 5: 112767212-112767218 (GRCh38) [ NCBI UCSC ] 5: 112102909-112102915 (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 Feb 8, 2023 Feb 20, 2024 Sep 1, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.244_250del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Phe82fs frameshift NM_001127510.3:c.244_250del NP_001120982.1:p.Phe82fs frameshift NM_001127511.3:c.274_280del NP_001120983.2:p.Phe92fs frameshift NM_001354895.2:c.244_250del NP_001341824.1:p.Phe82fs frameshift NM_001354896.2:c.244_250del NP_001341825.1:p.Phe82fs frameshift NM_001354897.2:c.274_280del NP_001341826.1:p.Phe92fs frameshift NM_001354898.2:c.169_175del NP_001341827.1:p.Phe57fs frameshift NM_001354899.2:c.244_250del NP_001341828.1:p.Phe82fs frameshift NM_001354900.2:c.67_73del NP_001341829.1:p.Phe23fs frameshift NM_001354901.2:c.67_73del NP_001341830.1:p.Phe23fs frameshift NM_001354902.2:c.274_280del NP_001341831.1:p.Phe92fs frameshift NM_001354903.2:c.244_250del NP_001341832.1:p.Phe82fs frameshift NM_001354904.2:c.169_175del NP_001341833.1:p.Phe57fs frameshift NM_001354905.2:c.67_73del NP_001341834.1:p.Phe23fs frameshift NM_001354906.2:c.-792_-786del 5 prime UTR NM_001407446.1:c.274_280delTTCCCTG NP_001394375.1:p.Phe92Glufs frameshift NM_001407447.1:c.244_250delTTCCCTG NP_001394376.1:p.Phe82Glufs frameshift NM_001407448.1:c.244_250delTTCCCTG NP_001394377.1:p.Phe82Glufs frameshift NM_001407449.1:c.244_250delTTCCCTG NP_001394378.1:p.Phe82Glufs frameshift NM_001407450.1:c.244_250delTTCCCTG NP_001394379.1:p.Phe82Glufs frameshift NM_001407451.1:c.169_175delTTCCCTG NP_001394380.1:p.Phe57Glufs frameshift NM_001407452.1:c.244_250delTTCCCTG NP_001394381.1:p.Phe82Glufs frameshift NM_001407453.1:c.67_73delTTCCCTG NP_001394382.1:p.Phe23Glufs frameshift NM_001407454.1:c.244_250delTTCCCTG NP_001394383.1:p.Phe82Glufs frameshift NM_001407455.1:c.244_250delTTCCCTG NP_001394384.1:p.Phe82Glufs frameshift NM_001407456.1:c.244_250delTTCCCTG NP_001394385.1:p.Phe82Glufs frameshift NM_001407457.1:c.244_250delTTCCCTG NP_001394386.1:p.Phe82Glufs frameshift NM_001407458.1:c.244_250delTTCCCTG NP_001394387.1:p.Phe82Glufs frameshift NM_001407459.1:c.244_250delTTCCCTG NP_001394388.1:p.Phe82Glufs frameshift NM_001407460.1:c.244_250delTTCCCTG NP_001394389.1:p.Phe82Glufs frameshift NM_001407467.1:c.244_250delTTCCCTG NP_001394396.1:p.Phe82Glufs frameshift NM_001407469.1:c.244_250delTTCCCTG NP_001394398.1:p.Phe82Glufs frameshift NM_001407470.1:c.-792_-786delTTCCCTG NM_001407471.1:c.-792_-786delTTCCCTG NM_001407472.1:c.-792_-786delTTCCCTG NR_176365.1:n.414_420delTTCCCTG NR_176366.1:n.647_653delTTCCCTG NC_000005.10:g.112767212_112767218del NC_000005.9:g.112102909_112102915del NG_008481.4:g.79692_79698del LRG_130:g.79692_79698del LRG_130t1:c.244_250del LRG_130p1:p.Phe82Glufs LRG_130t2:c.244_250del LRG_130p2:p.Phe82Glufs LRG_130t3:c.244_250del LRG_130p3:p.Phe82Glufs - Protein change
- F82fs, F23fs, F57fs, F92fs
- Other names
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- Canonical SPDI
- NC_000005.10:112767211:TTCCCTG:
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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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APC | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
14000 | 14134 |
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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Pathogenic (1) |
criteria provided, single submitter
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Sep 1, 2022 | RCV003744869.1 |
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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Pathogenic
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
Affected status: unknown
Allele origin:
germline
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Invitae
Accession: SCV003312570.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with APC-related conditions. … (more)
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Phe82Glufs*2) in the APC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668). (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
HelpTitle | Author | Journal | Year | Link |
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Germline APC mutation spectrum derived from 863 genomic variations identified through a 15-year medical genetics service to French patients with FAP. | Lagarde A | Journal of medical genetics | 2010 | PMID: 20685668 |
Mutational screening of the APC gene in Chilean families with familial adenomatous polyposis: nine novel truncating mutations. | De la Fuente MK | Diseases of the colon and rectum | 2007 | PMID: 17963004 |
Text-mined citations for this variant ...
HelpRecord last updated Apr 15, 2024
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.