ACMG Criteria: PVS1,PM2_SUP
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.6239dup (p.Leu2080fs)
Germline
Classification
Help
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.
(1)
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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.
Likely pathogenic
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000038.6(APC):c.6239dup (p.Leu2080fs)
Variation ID: 3235960 Accession: VCV003235960.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112841830-112841831 (GRCh38) [ NCBI UCSC ] 5: 112177527-112177528 (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 May 19, 2024 May 19, 2024 May 16, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.6239dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Leu2080fs frameshift NM_001127510.3:c.6239dup NP_001120982.1:p.Leu2080fs frameshift NM_001127511.3:c.6185dup NP_001120983.2:p.Leu2062fs frameshift NM_001354895.2:c.6239dup NP_001341824.1:p.Leu2080fs frameshift NM_001354896.2:c.6293dup NP_001341825.1:p.Leu2098fs frameshift NM_001354897.2:c.6269dup NP_001341826.1:p.Leu2090fs frameshift NM_001354898.2:c.6164dup NP_001341827.1:p.Leu2055fs frameshift NM_001354899.2:c.6155dup NP_001341828.1:p.Leu2052fs frameshift NM_001354900.2:c.6116dup NP_001341829.1:p.Leu2039fs frameshift NM_001354901.2:c.6062dup NP_001341830.1:p.Leu2021fs frameshift NM_001354902.2:c.5966dup NP_001341831.1:p.Leu1989fs frameshift NM_001354903.2:c.5936dup NP_001341832.1:p.Leu1979fs frameshift NM_001354904.2:c.5861dup NP_001341833.1:p.Leu1954fs frameshift NM_001354905.2:c.5759dup NP_001341834.1:p.Leu1920fs frameshift NM_001354906.2:c.5390dup NP_001341835.1:p.Leu1797fs frameshift NM_001407446.1:c.6323dup NP_001394375.1:p.Leu2108fs frameshift NM_001407447.1:c.6293dup NP_001394376.1:p.Leu2098fs frameshift NM_001407448.1:c.6293dup NP_001394377.1:p.Leu2098fs frameshift NM_001407449.1:c.6293dup NP_001394378.1:p.Leu2098fs frameshift NM_001407450.1:c.6239dup NP_001394379.1:p.Leu2080fs frameshift NM_001407451.1:c.6218dup NP_001394380.1:p.Leu2073fs frameshift NM_001407452.1:c.6209dup NP_001394381.1:p.Leu2070fs frameshift NM_001407453.1:c.6062dup NP_001394382.1:p.Leu2021fs frameshift NM_001407454.1:c.5990dup NP_001394383.1:p.Leu1997fs frameshift NM_001407455.1:c.5990dup NP_001394384.1:p.Leu1997fs frameshift NM_001407456.1:c.5990dup NP_001394385.1:p.Leu1997fs frameshift NM_001407457.1:c.5990dup NP_001394386.1:p.Leu1997fs frameshift NM_001407458.1:c.5936dup NP_001394387.1:p.Leu1979fs frameshift NM_001407459.1:c.5936dup NP_001394388.1:p.Leu1979fs frameshift NM_001407460.1:c.5936dup NP_001394389.1:p.Leu1979fs frameshift NM_001407467.1:c.5852dup NP_001394396.1:p.Leu1951fs frameshift NM_001407469.1:c.5852dup NP_001394398.1:p.Leu1951fs frameshift NM_001407470.1:c.5390dup NP_001394399.1:p.Leu1797fs frameshift NM_001407471.1:c.5087dup NP_001394400.1:p.Leu1696fs frameshift NM_001407472.1:c.5087dup NP_001394401.1:p.Leu1696fs frameshift NR_176365.1:n.6074dup non-coding transcript variant NR_176366.1:n.6493dup non-coding transcript variant NC_000005.10:g.112841833dup NC_000005.9:g.112177530dup NG_008481.4:g.154313dup LRG_130:g.154313dup LRG_130t1:c.6239dup LRG_130p1:p.Leu2080Phefs LRG_130t2:c.6239dup LRG_130p2:p.Leu2080Phefs LRG_130t3:c.6239dup LRG_130p3:p.Leu2080Phefs - Protein change
- L1696fs, L1797fs, L1920fs, L1951fs, L1954fs, L1979fs, L1989fs, L1997fs, L2021fs, L2039fs, L2052fs, L2055fs, L2062fs, L2070fs, L2073fs, L2080fs, L2090fs, L2098fs, L2108fs
- Other names
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- Canonical SPDI
- NC_000005.10:112841830:TTT:TTTT
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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
Help
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
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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 |
14981 | 15119 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
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
Help
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. |
|---|---|---|---|---|
| Likely pathogenic (1) |
criteria provided, single submitter
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May 16, 2023 | RCV004555221.2 |
Submissions - Germline
| Classification
Help
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
Help
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
Help
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
(May 16, 2023)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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MVZ Medizinische Genetik Mainz
Accession: SCV005044194.1
First in ClinVar: May 19, 2024 Last updated: May 19, 2024 |
Comment:
ACMG Criteria: PVS1,PM2_SUP
Number of individuals with the variant: 1
Clinical Features:
Colon cancer (present) , Adenomatous colonic polyposis (present) , Testicular neoplasm (present) , Large intestinal polyposis (present) , Colonic neoplasm (present) , Colorectal polyposis (present)
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Comment:
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. |
Comment:
ACMG Criteria: PVS1,PM2_SUP
Citations for germline classification of this variant
Help| There 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 Jun 02, 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.