ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.5310_5374del (p.Lys1771fs)
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.5310_5374del (p.Lys1771fs)
Variation ID: 2583496 Accession: VCV002583496.2
- Type and length
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Deletion, 65 bp
- Location
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Cytogenetic: 5q22.2 5: 112840894-112840958 (GRCh38) [ NCBI UCSC ] 5: 112176591-112176655 (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 21, 2023 Oct 28, 2023 May 12, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.5310_5374del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Lys1771fs frameshift NM_001127510.3:c.5310_5374del NP_001120982.1:p.Lys1771fs frameshift NM_001127511.3:c.5256_5320del NP_001120983.2:p.Lys1753fs frameshift NM_001354895.2:c.5310_5374del NP_001341824.1:p.Lys1771fs frameshift NM_001354896.2:c.5364_5428del NP_001341825.1:p.Lys1789fs frameshift NM_001354897.2:c.5340_5404del NP_001341826.1:p.Lys1781fs frameshift NM_001354898.2:c.5235_5299del NP_001341827.1:p.Lys1746fs frameshift NM_001354899.2:c.5226_5290del NP_001341828.1:p.Lys1743fs frameshift NM_001354900.2:c.5187_5251del NP_001341829.1:p.Lys1730fs frameshift NM_001354901.2:c.5133_5197del NP_001341830.1:p.Lys1712fs frameshift NM_001354902.2:c.5037_5101del NP_001341831.1:p.Lys1680fs frameshift NM_001354903.2:c.5007_5071del NP_001341832.1:p.Lys1670fs frameshift NM_001354904.2:c.4932_4996del NP_001341833.1:p.Lys1645fs frameshift NM_001354905.2:c.4830_4894del NP_001341834.1:p.Lys1611fs frameshift NM_001354906.2:c.4461_4525del NP_001341835.1:p.Lys1488fs frameshift NM_001407446.1:c.5394_5458del NP_001394375.1:p.Lys1799fs frameshift NM_001407447.1:c.5364_5428del NP_001394376.1:p.Lys1789fs frameshift NM_001407448.1:c.5364_5428del NP_001394377.1:p.Lys1789fs frameshift NM_001407449.1:c.5364_5428del NP_001394378.1:p.Lys1789fs frameshift NM_001407450.1:c.5310_5374del NP_001394379.1:p.Lys1771fs frameshift NM_001407451.1:c.5289_5353del NP_001394380.1:p.Lys1764fs frameshift NM_001407452.1:c.5280_5344del NP_001394381.1:p.Lys1761fs frameshift NM_001407453.1:c.5133_5197del NP_001394382.1:p.Lys1712fs frameshift NM_001407454.1:c.5061_5125del NP_001394383.1:p.Lys1688fs frameshift NM_001407455.1:c.5061_5125del NP_001394384.1:p.Lys1688fs frameshift NM_001407456.1:c.5061_5125del NP_001394385.1:p.Lys1688fs frameshift NM_001407457.1:c.5061_5125del NP_001394386.1:p.Lys1688fs frameshift NM_001407458.1:c.5007_5071del NP_001394387.1:p.Lys1670fs frameshift NM_001407459.1:c.5007_5071del NP_001394388.1:p.Lys1670fs frameshift NM_001407460.1:c.5007_5071del NP_001394389.1:p.Lys1670fs frameshift NM_001407467.1:c.4923_4987del NP_001394396.1:p.Lys1642fs frameshift NM_001407469.1:c.4923_4987del NP_001394398.1:p.Lys1642fs frameshift NM_001407470.1:c.4461_4525del NP_001394399.1:p.Lys1488fs frameshift NM_001407471.1:c.4158_4222del NP_001394400.1:p.Lys1387fs frameshift NM_001407472.1:c.4158_4222del NP_001394401.1:p.Lys1387fs frameshift NR_176365.1:n.5145_5209del non-coding transcript variant NR_176366.1:n.5564_5628del non-coding transcript variant NC_000005.10:g.112840904_112840968del NC_000005.9:g.112176601_112176665del NG_008481.4:g.153384_153448del LRG_130:g.153384_153448del LRG_130t1:c.5310_5374del65 LRG_130p1:p.Lys1771Cysfs LRG_130t2:c.5310_5374del65 LRG_130p2:p.Lys1771Cysfs LRG_130t3:c.5310_5374del65 LRG_130p3:p.Lys1771Cysfs - Protein change
- K1387fs, K1488fs, K1611fs, K1642fs, K1645fs, K1670fs, K1680fs, K1688fs, K1712fs, K1730fs, K1743fs, K1746fs, K1753fs, K1761fs, K1764fs, K1771fs, K1781fs, K1789fs, K1799fs
- Other names
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- Canonical SPDI
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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 |
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
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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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May 12, 2023 | RCV004566141.1 |
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
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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
(May 12, 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: SCV004045339.2
First in ClinVar: Oct 21, 2023 Last updated: Oct 28, 2023 |
Comment:
This variant is considered pathogenic. This variant creates a frameshift 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
HelpThere 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 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.