ClinGen APC VCEP: PVS1, PM2_Supporting
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.5038_5039del (p.Gln1680fs)
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.5038_5039del (p.Gln1680fs)
Variation ID: 3340529 Accession: VCV003340529.1
- Type and length
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Microsatellite, 2 bp
- Location
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Cytogenetic: 5q22.2 5: 112840630-112840631 (GRCh38) [ NCBI UCSC ] 5: 112176327-112176328 (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 Oct 8, 2024 Oct 8, 2024 Sep 24, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.5038_5039del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Gln1680fs frameshift NM_001127510.3:c.5038_5039del NP_001120982.1:p.Gln1680fs frameshift NM_001127511.3:c.4984_4985del NP_001120983.2:p.Gln1662fs frameshift NM_001354895.2:c.5038_5039del NP_001341824.1:p.Gln1680fs frameshift NM_001354896.2:c.5092_5093del NP_001341825.1:p.Gln1698fs frameshift NM_001354897.2:c.5068_5069del NP_001341826.1:p.Gln1690fs frameshift NM_001354898.2:c.4963_4964del NP_001341827.1:p.Gln1655fs frameshift NM_001354899.2:c.4954_4955del NP_001341828.1:p.Gln1652fs frameshift NM_001354900.2:c.4915_4916del NP_001341829.1:p.Gln1639fs frameshift NM_001354901.2:c.4861_4862del NP_001341830.1:p.Gln1621fs frameshift NM_001354902.2:c.4765_4766del NP_001341831.1:p.Gln1589fs frameshift NM_001354903.2:c.4735_4736del NP_001341832.1:p.Gln1579fs frameshift NM_001354904.2:c.4660_4661del NP_001341833.1:p.Gln1554fs frameshift NM_001354905.2:c.4558_4559del NP_001341834.1:p.Gln1520fs frameshift NM_001354906.2:c.4189_4190del NP_001341835.1:p.Gln1397fs frameshift NM_001407446.1:c.5122_5123del NP_001394375.1:p.Gln1708fs frameshift NM_001407447.1:c.5092_5093del NP_001394376.1:p.Gln1698fs frameshift NM_001407448.1:c.5092_5093del NP_001394377.1:p.Gln1698fs frameshift NM_001407449.1:c.5092_5093del NP_001394378.1:p.Gln1698fs frameshift NM_001407450.1:c.5038_5039del NP_001394379.1:p.Gln1680fs frameshift NM_001407451.1:c.5017_5018del NP_001394380.1:p.Gln1673fs frameshift NM_001407452.1:c.5008_5009del NP_001394381.1:p.Gln1670fs frameshift NM_001407453.1:c.4861_4862del NP_001394382.1:p.Gln1621fs frameshift NM_001407454.1:c.4789_4790del NP_001394383.1:p.Gln1597fs frameshift NM_001407455.1:c.4789_4790del NP_001394384.1:p.Gln1597fs frameshift NM_001407456.1:c.4789_4790del NP_001394385.1:p.Gln1597fs frameshift NM_001407457.1:c.4789_4790del NP_001394386.1:p.Gln1597fs frameshift NM_001407458.1:c.4735_4736del NP_001394387.1:p.Gln1579fs frameshift NM_001407459.1:c.4735_4736del NP_001394388.1:p.Gln1579fs frameshift NM_001407460.1:c.4735_4736del NP_001394389.1:p.Gln1579fs frameshift NM_001407467.1:c.4651_4652del NP_001394396.1:p.Gln1551fs frameshift NM_001407469.1:c.4651_4652del NP_001394398.1:p.Gln1551fs frameshift NM_001407470.1:c.4189_4190del NP_001394399.1:p.Gln1397fs frameshift NM_001407471.1:c.3886_3887del NP_001394400.1:p.Gln1296fs frameshift NM_001407472.1:c.3886_3887del NP_001394401.1:p.Gln1296fs frameshift NR_176365.1:n.4871CA[1] non-coding transcript variant NR_176366.1:n.5290CA[1] non-coding transcript variant NC_000005.10:g.112840630CA[1] NC_000005.9:g.112176327CA[1] NG_008481.4:g.153110CA[1] LRG_130:g.153110CA[1] LRG_130t1:c.5036_5037CA[1] LRG_130p1:p.Gln1680Valfs LRG_130t2:c.5036_5037CA[1] LRG_130p2:p.Gln1680Valfs LRG_130t3:c.5036_5037CA[1] LRG_130p3:p.Gln1680Valfs - Protein change
- Q1296fs, Q1397fs, Q1520fs, Q1551fs, Q1554fs, Q1579fs, Q1589fs, Q1597fs, Q1621fs, Q1639fs, Q1652fs, Q1655fs, Q1662fs, Q1670fs, Q1673fs, Q1680fs, Q1690fs, Q1698fs, Q1708fs
- Other names
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- Canonical SPDI
- NC_000005.10:112840629:CACA:CA
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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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Sep 24, 2024 | RCV004720571.1 |
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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|---|---|---|---|---|---|
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Likely pathogenic
(Sep 24, 2024)
|
criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Department of Human Genetics, Hannover Medical School
Accession: SCV005326554.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
ClinGen APC VCEP: PVS1, PM2_Supporting
Clinical Features:
Adenomatous colonic polyposis (present)
|
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:
ClinGen APC VCEP: PVS1, PM2_Supporting
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 Oct 08, 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.