ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.7054A>T (p.Ser2352Cys)
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.7054A>T (p.Ser2352Cys)
Variation ID: 3231143 Accession: VCV003231143.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112842648 (GRCh38) [ NCBI UCSC ] 5: 112178345 (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 1, 2024 May 1, 2024 Feb 16, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000038.6:c.7054A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Ser2352Cys missense NM_001127510.3:c.7054A>T NP_001120982.1:p.Ser2352Cys missense NM_001127511.3:c.7000A>T NP_001120983.2:p.Ser2334Cys missense NM_001354895.2:c.7054A>T NP_001341824.1:p.Ser2352Cys missense NM_001354896.2:c.7108A>T NP_001341825.1:p.Ser2370Cys missense NM_001354897.2:c.7084A>T NP_001341826.1:p.Ser2362Cys missense NM_001354898.2:c.6979A>T NP_001341827.1:p.Ser2327Cys missense NM_001354899.2:c.6970A>T NP_001341828.1:p.Ser2324Cys missense NM_001354900.2:c.6931A>T NP_001341829.1:p.Ser2311Cys missense NM_001354901.2:c.6877A>T NP_001341830.1:p.Ser2293Cys missense NM_001354902.2:c.6781A>T NP_001341831.1:p.Ser2261Cys missense NM_001354903.2:c.6751A>T NP_001341832.1:p.Ser2251Cys missense NM_001354904.2:c.6676A>T NP_001341833.1:p.Ser2226Cys missense NM_001354905.2:c.6574A>T NP_001341834.1:p.Ser2192Cys missense NM_001354906.2:c.6205A>T NP_001341835.1:p.Ser2069Cys missense NM_001407446.1:c.7138A>T NP_001394375.1:p.Ser2380Cys missense NM_001407447.1:c.7108A>T NP_001394376.1:p.Ser2370Cys missense NM_001407448.1:c.7108A>T NP_001394377.1:p.Ser2370Cys missense NM_001407449.1:c.7108A>T NP_001394378.1:p.Ser2370Cys missense NM_001407450.1:c.7054A>T NP_001394379.1:p.Ser2352Cys missense NM_001407451.1:c.7033A>T NP_001394380.1:p.Ser2345Cys missense NM_001407452.1:c.7024A>T NP_001394381.1:p.Ser2342Cys missense NM_001407453.1:c.6877A>T NP_001394382.1:p.Ser2293Cys missense NM_001407454.1:c.6805A>T NP_001394383.1:p.Ser2269Cys missense NM_001407455.1:c.6805A>T NP_001394384.1:p.Ser2269Cys missense NM_001407456.1:c.6805A>T NP_001394385.1:p.Ser2269Cys missense NM_001407457.1:c.6805A>T NP_001394386.1:p.Ser2269Cys missense NM_001407458.1:c.6751A>T NP_001394387.1:p.Ser2251Cys missense NM_001407459.1:c.6751A>T NP_001394388.1:p.Ser2251Cys missense NM_001407460.1:c.6751A>T NP_001394389.1:p.Ser2251Cys missense NM_001407467.1:c.6667A>T NP_001394396.1:p.Ser2223Cys missense NM_001407469.1:c.6667A>T NP_001394398.1:p.Ser2223Cys missense NM_001407470.1:c.6205A>T NP_001394399.1:p.Ser2069Cys missense NM_001407471.1:c.5902A>T NP_001394400.1:p.Ser1968Cys missense NM_001407472.1:c.5902A>T NP_001394401.1:p.Ser1968Cys missense NR_176365.1:n.6889A>T non-coding transcript variant NR_176366.1:n.7308A>T non-coding transcript variant NC_000005.10:g.112842648A>T NC_000005.9:g.112178345A>T NG_008481.4:g.155128A>T LRG_130:g.155128A>T LRG_130t1:c.7054A>T LRG_130p1:p.Ser2352Cys LRG_130t2:c.7054A>T LRG_130p2:p.Ser2352Cys LRG_130t3:c.7054A>T LRG_130p3:p.Ser2352Cys - Protein change
- S1968C, S2069C, S2192C, S2223C, S2226C, S2251C, S2261C, S2269C, S2293C, S2311C, S2324C, S2327C, S2334C, S2342C, S2345C, S2352C, S2362C, S2370C, S2380C
- Other names
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- Canonical SPDI
- NC_000005.10:112842647:A: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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- 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 | ||
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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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Uncertain significance (1) |
criteria provided, single submitter
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Feb 16, 2024 | RCV004525214.1 |
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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Uncertain significance
(Feb 16, 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: SCV005034349.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The p.S2352C variant (also known as c.7054A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide … (more)
The p.S2352C variant (also known as c.7054A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide position 7054. The serine at codon 2352 is replaced by cysteine, an amino acid with dissimilar properties. This amino acid position is conserved. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Based on the available evidence, the clinical significance of this alteration remains unclear. (less)
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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 May 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.