ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.287dup (p.Tyr96Ter)
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.287dup (p.Tyr96Ter)
Variation ID: 1797156 Accession: VCV001797156.1
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112767254-112767255 (GRCh38) [ NCBI UCSC ] 5: 112102951-112102952 (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 29, 2022 Nov 29, 2022 Jul 10, 2020 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.287dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Tyr96Ter nonsense NM_001127510.3:c.287dup NP_001120982.1:p.Tyr96Ter nonsense NM_001127511.3:c.317dup NP_001120983.2:p.Tyr106Ter nonsense NM_001354895.2:c.287dup NP_001341824.1:p.Tyr96Ter nonsense NM_001354896.2:c.287dup NP_001341825.1:p.Tyr96Ter nonsense NM_001354897.2:c.317dup NP_001341826.1:p.Tyr106Ter nonsense NM_001354898.2:c.212dup NP_001341827.1:p.Tyr71Ter nonsense NM_001354899.2:c.287dup NP_001341828.1:p.Tyr96Ter nonsense NM_001354900.2:c.110dup NP_001341829.1:p.Tyr37Ter nonsense NM_001354901.2:c.110dup NP_001341830.1:p.Tyr37Ter nonsense NM_001354902.2:c.317dup NP_001341831.1:p.Tyr106Ter nonsense NM_001354903.2:c.287dup NP_001341832.1:p.Tyr96Ter nonsense NM_001354904.2:c.212dup NP_001341833.1:p.Tyr71Ter nonsense NM_001354905.2:c.110dup NP_001341834.1:p.Tyr37Ter nonsense NM_001354906.2:c.-749dup 5 prime UTR NM_001407446.1:c.317dup NP_001394375.1:p.Tyr106Terfs frameshift nonsense NM_001407447.1:c.287dup NP_001394376.1:p.Tyr96Terfs frameshift nonsense NM_001407448.1:c.287dup NP_001394377.1:p.Tyr96Terfs frameshift nonsense NM_001407449.1:c.287dup NP_001394378.1:p.Tyr96Terfs frameshift nonsense NM_001407450.1:c.287dup NP_001394379.1:p.Tyr96Terfs frameshift nonsense NM_001407451.1:c.212dup NP_001394380.1:p.Tyr71Terfs frameshift nonsense NM_001407452.1:c.287dup NP_001394381.1:p.Tyr96Terfs frameshift nonsense NM_001407453.1:c.110dup NP_001394382.1:p.Tyr37Terfs frameshift nonsense NM_001407454.1:c.287dup NP_001394383.1:p.Tyr96Terfs frameshift nonsense NM_001407455.1:c.287dup NP_001394384.1:p.Tyr96Terfs frameshift nonsense NM_001407456.1:c.287dup NP_001394385.1:p.Tyr96Terfs frameshift nonsense NM_001407457.1:c.287dup NP_001394386.1:p.Tyr96Terfs frameshift nonsense NM_001407458.1:c.287dup NP_001394387.1:p.Tyr96Terfs frameshift nonsense NM_001407459.1:c.287dup NP_001394388.1:p.Tyr96Terfs frameshift nonsense NM_001407460.1:c.287dup NP_001394389.1:p.Tyr96Terfs frameshift nonsense NM_001407467.1:c.287dup NP_001394396.1:p.Tyr96Terfs frameshift nonsense NM_001407469.1:c.287dup NP_001394398.1:p.Tyr96Terfs frameshift nonsense NM_001407470.1:c.-749dup NM_001407471.1:c.-749dup NM_001407472.1:c.-749dup NR_176365.1:n.457dup NR_176366.1:n.690dup NC_000005.10:g.112767255dup NC_000005.9:g.112102952dup NG_008481.4:g.79735dup LRG_130:g.79735dup LRG_130t1:c.287dup LRG_130p1:p.Tyr96Terfs LRG_130t2:c.287dup LRG_130p2:p.Tyr96Terfs LRG_130t3:c.287dup LRG_130p3:p.Tyr96Terfs - Protein change
- Y71*, Y106*, Y96*, Y37*
- Other names
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- Canonical SPDI
- NC_000005.10:112767254:A:AA
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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
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
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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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Jul 10, 2020 | RCV002437781.1 |
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
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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
(Jul 10, 2020)
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criteria provided, single submitter
Method: clinical testing
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Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002749574.1
First in ClinVar: Nov 29, 2022 Last updated: Nov 29, 2022 |
Comment:
The c.287dupA pathogenic mutation (also known as p.Y96*), located in coding exon 3 of the APC gene, results from a duplication of A at nucleotide … (more)
The c.287dupA pathogenic mutation (also known as p.Y96*), located in coding exon 3 of the APC gene, results from a duplication of A at nucleotide position 287. This changes the amino acid from a tyrosine to a stop codon within coding exon 3. In a large (n=1591) series of patients referred for APC testing, this alteration was detected in one individual (Kerr SE et al. J. Mol. Diagn. 2013 Jan;15:31-43). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. (less)
Number of individuals with the variant: 1
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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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APC germline mutations in individuals being evaluated for familial adenomatous polyposis: a review of the Mayo Clinic experience with 1591 consecutive tests. | Kerr SE | The Journal of molecular diagnostics : JMD | 2013 | PMID: 23159591 |
Text-mined citations for this variant ...
HelpRecord last updated Dec 25, 2023
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.