ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.3404_3405del (p.Asp1134_Tyr1135insTer)
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.3404_3405del (p.Asp1134_Tyr1135insTer)
Variation ID: 219434 Accession: VCV000219434.12
- Type and length
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Deletion, 2 bp
- Location
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Cytogenetic: 5q22.2 5: 112838997-112838998 (GRCh38) [ NCBI UCSC ] 5: 112174694-112174695 (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 2, 2016 May 1, 2024 Feb 20, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.3404_3405del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Asp1134_Tyr1135insTer nonsense NM_001127510.3:c.3404_3405del NP_001120982.1:p.Asp1134_Tyr1135insTer nonsense NM_001127511.3:c.3350_3351del NP_001120983.2:p.Asp1116_Tyr1117insTer nonsense NM_001354895.2:c.3404_3405del NP_001341824.1:p.Asp1134_Tyr1135insTer nonsense NM_001354896.2:c.3458_3459del NP_001341825.1:p.Asp1152_Tyr1153insTer nonsense NM_001354897.2:c.3434_3435del NP_001341826.1:p.Asp1144_Tyr1145insTer nonsense NM_001354898.2:c.3329_3330del NP_001341827.1:p.Asp1109_Tyr1110insTer nonsense NM_001354899.2:c.3320_3321del NP_001341828.1:p.Asp1106_Tyr1107insTer nonsense NM_001354900.2:c.3281_3282del NP_001341829.1:p.Asp1093_Tyr1094insTer nonsense NM_001354901.2:c.3227_3228del NP_001341830.1:p.Asp1075_Tyr1076insTer nonsense NM_001354902.2:c.3131_3132del NP_001341831.1:p.Asp1043_Tyr1044insTer nonsense NM_001354903.2:c.3101_3102del NP_001341832.1:p.Asp1033_Tyr1034insTer nonsense NM_001354904.2:c.3026_3027del NP_001341833.1:p.Asp1008_Tyr1009insTer nonsense NM_001354905.2:c.2924_2925del NP_001341834.1:p.Asp974_Tyr975insTer nonsense NM_001354906.2:c.2555_2556del NP_001341835.1:p.Asp851_Tyr852insTer nonsense NC_000005.10:g.112838998_112838999del NC_000005.9:g.112174695_112174696del NG_008481.4:g.151478_151479del LRG_130:g.151478_151479del - Protein change
- Other names
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- Canonical SPDI
- NC_000005.10:112838996:TAT:T
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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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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 | ||
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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
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 |
14956 | 15094 |
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. |
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Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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May 8, 2023 | RCV003335225.4 | |
Pathogenic (1) |
criteria provided, single submitter
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Feb 20, 2024 | RCV004020501.1 |
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
Help
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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Pathogenic
(Feb 20, 2024)
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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: SCV005031169.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The c.3404_3405delAT pathogenic mutation, located in coding exon 15 of the APC gene, results from a deletion of two nucleotides at nucleotide positions 3404 to … (more)
The c.3404_3405delAT pathogenic mutation, located in coding exon 15 of the APC gene, results from a deletion of two nucleotides at nucleotide positions 3404 to 3405, causing a translational frameshift with a predicted alternate stop codon (p.Y1135*). This alteration occurs at the 3' terminus of theAPC gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 60.1% of the protein. However, premature stop codons are typically deleterious in nature and the impacted region is critical for protein function (Ambry internal data). This variant has been observed in multiple individuals with a personal and/or family history that is consistent with APC-associated polyposis conditions (Staninova-Stojovska M et al. Balkan J Med Genet, 2019 Dec;22:5-16; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(Feb 27, 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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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000259299.7
First in ClinVar: Feb 02, 2016 Last updated: Feb 28, 2024 |
Comment:
This variant is expected to disrupt the EB1 and HDLG binding sites, which mediate interactions with the cytoskeleton (PMID: 15311282, 17293347). While functional studies have … (more)
This variant is expected to disrupt the EB1 and HDLG binding sites, which mediate interactions with the cytoskeleton (PMID: 15311282, 17293347). While functional studies have not been performed to directly test the effect on APC protein function, this suggests that disruption of the C-terminal portion of the protein is functionally important. For these reasons, this variant has been classified as Pathogenic. A different truncation (p.Tyr2645Lysfs*14) that lies downstream of this variant has been determined to be pathogenic (PMID: 9824584, 1316610, 27081525, 8381579, 22135120, Invitae). This suggests that deletion of this region of the APC protein is causative of disease. ClinVar contains an entry for this variant (Variation ID: 219434). This premature translational stop signal has been observed in individual(s) with clinical features of familial adenomatous polyposis (PMID: 8730280, 11748858). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr1135*) in the APC gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 1709 amino acid(s) of the APC protein. (less)
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Pathogenic
(May 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Familial adenomatous polyposis 1
Affected status: unknown
Allele origin:
unknown
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Myriad Genetics, Inc.
Accession: SCV004043166.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation.
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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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Molecular Basis of Inherited Colorectal Carcinomas in the Macedonian Population: An Update. | Staninova-Stojovska M | Balkan journal of medical genetics : BJMG | 2019 | PMID: 31942411 |
Attenuated familial adenomatous polyposis with desmoids caused by an APC mutation. | Ikenoue T | Human genome variation | 2015 | PMID: 27081525 |
Prevalence of skin lesions in familial adenomatous polyposis: a marker for presymptomatic diagnosis? | Burger B | The oncologist | 2011 | PMID: 22135120 |
Regulated binding of adenomatous polyposis coli protein to actin. | Moseley JB | The Journal of biological chemistry | 2007 | PMID: 17293347 |
EB1 and APC bind to mDia to stabilize microtubules downstream of Rho and promote cell migration. | Wen Y | Nature cell biology | 2004 | PMID: 15311282 |
Molecular and clinical characteristics in 32 families affected with familial adenomatous polyposis. | Hutter P | Human mutation | 2001 | PMID: 11748858 |
Variable phenotype of familial adenomatous polyposis in pedigrees with 3' mutation in the APC gene. | Brensinger JD | Gut | 1998 | PMID: 9824584 |
Correlation between the development of extracolonic manifestations in FAP patients and mutations beyond codon 1403 in the APC gene. | Dobbie Z | Journal of medical genetics | 1996 | PMID: 8730280 |
Mutational analysis of patients with adenomatous polyposis: identical inactivating mutations in unrelated individuals. | Groden J | American journal of human genetics | 1993 | PMID: 8381579 |
Germ-line mutations of the APC gene in 53 familial adenomatous polyposis patients. | Miyoshi Y | Proceedings of the National Academy of Sciences of the United States of America | 1992 | PMID: 1316610 |
Text-mined citations for rs864622086 ...
HelpRecord last updated Oct 13, 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.