The p.V1125G variant (also known as c.3374T>G), located in coding exon 15 of the APC gene, results from a T to G substitution at nucleotide position 3374. The valine at codon 1125 is replaced by glycine, an amino acid with dissimilar properties. This variant was detected in 1 of 1292 individuals with biliary tract cancer and 2 of 37583 controls without a personal or family history of biliary tract cancer in Japan (Okawa Y et al. J Hepatol, 2023 Feb;78:333-342).This amino acid position is well conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Missense alterations in APC are not a common cause of disease (Spier I et al. Genet Med. 2024 Feb;26(2):100992). Based on the available evidence, the clinical significance of this variant remains unclear.
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.3374T>G (p.Val1125Gly)
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.
Uncertain significance
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.3374T>G (p.Val1125Gly)
Variation ID: 3411437 Accession: VCV003411437.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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5: 112838968 (GRCh38) [ NCBI UCSC ] 5: 112174665 (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 Jan 13, 2025 Jan 13, 2025 Oct 10, 2024 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.3374T>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Val1125Gly missense NM_001127510.3:c.3374T>G NP_001120982.1:p.Val1125Gly missense NM_001127511.3:c.3320T>G NP_001120983.2:p.Val1107Gly missense NM_001354895.2:c.3374T>G NP_001341824.1:p.Val1125Gly missense NM_001354896.2:c.3428T>G NP_001341825.1:p.Val1143Gly missense NM_001354897.2:c.3404T>G NP_001341826.1:p.Val1135Gly missense NM_001354898.2:c.3299T>G NP_001341827.1:p.Val1100Gly missense NM_001354899.2:c.3290T>G NP_001341828.1:p.Val1097Gly missense NM_001354900.2:c.3251T>G NP_001341829.1:p.Val1084Gly missense NM_001354901.2:c.3197T>G NP_001341830.1:p.Val1066Gly missense NM_001354902.2:c.3101T>G NP_001341831.1:p.Val1034Gly missense NM_001354903.2:c.3071T>G NP_001341832.1:p.Val1024Gly missense NM_001354904.2:c.2996T>G NP_001341833.1:p.Val999Gly missense NM_001354905.2:c.2894T>G NP_001341834.1:p.Val965Gly missense NM_001354906.2:c.2525T>G NP_001341835.1:p.Val842Gly missense NM_001407446.1:c.3458T>G NP_001394375.1:p.Val1153Gly missense NM_001407447.1:c.3428T>G NP_001394376.1:p.Val1143Gly missense NM_001407448.1:c.3428T>G NP_001394377.1:p.Val1143Gly missense NM_001407449.1:c.3428T>G NP_001394378.1:p.Val1143Gly missense NM_001407450.1:c.3374T>G NP_001394379.1:p.Val1125Gly missense NM_001407451.1:c.3353T>G NP_001394380.1:p.Val1118Gly missense NM_001407452.1:c.3344T>G NP_001394381.1:p.Val1115Gly missense NM_001407453.1:c.3197T>G NP_001394382.1:p.Val1066Gly missense NM_001407454.1:c.3125T>G NP_001394383.1:p.Val1042Gly missense NM_001407455.1:c.3125T>G NP_001394384.1:p.Val1042Gly missense NM_001407456.1:c.3125T>G NP_001394385.1:p.Val1042Gly missense NM_001407457.1:c.3125T>G NP_001394386.1:p.Val1042Gly missense NM_001407458.1:c.3071T>G NP_001394387.1:p.Val1024Gly missense NM_001407459.1:c.3071T>G NP_001394388.1:p.Val1024Gly missense NM_001407460.1:c.3071T>G NP_001394389.1:p.Val1024Gly missense NM_001407467.1:c.2987T>G NP_001394396.1:p.Val996Gly missense NM_001407469.1:c.2987T>G NP_001394398.1:p.Val996Gly missense NM_001407470.1:c.2525T>G NP_001394399.1:p.Val842Gly missense NM_001407471.1:c.2222T>G NP_001394400.1:p.Val741Gly missense NM_001407472.1:c.2222T>G NP_001394401.1:p.Val741Gly missense NR_176365.1:n.3209T>G non-coding transcript variant NR_176366.1:n.3628T>G non-coding transcript variant NC_000005.10:g.112838968T>G NC_000005.9:g.112174665T>G NG_008481.4:g.151448T>G LRG_130:g.151448T>G LRG_130t1:c.3374T>G LRG_130p1:p.Val1125Gly LRG_130t2:c.3374T>G LRG_130p2:p.Val1125Gly LRG_130t3:c.3374T>G LRG_130p3:p.Val1125Gly - Protein change
- V1115G, V1118G, V1125G, V1143G, V741G, V1024G, V1107G, V1135G, V1153G, V965G, V1034G, V1042G, V1084G, V1100G, V999G, V1066G, V1097G, V842G, V996G
- Other names
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- Canonical SPDI
- NC_000005.10:112838967:T:G
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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 |
15241 | 15379 | |
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Oct 10, 2024 | RCV004945490.1 |
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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Uncertain significance
(Oct 10, 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: SCV005467109.1
First in ClinVar: Jan 13, 2025 Last updated: Jan 13, 2025 |
Comment:
The p.V1125G variant (also known as c.3374T>G), located in coding exon 15 of the APC gene, results from a T to G substitution at nucleotide … (more)
The p.V1125G variant (also known as c.3374T>G), located in coding exon 15 of the APC gene, results from a T to G substitution at nucleotide position 3374. The valine at codon 1125 is replaced by glycine, an amino acid with dissimilar properties. This variant was detected in 1 of 1292 individuals with biliary tract cancer and 2 of 37583 controls without a personal or family history of biliary tract cancer in Japan (Okawa Y et al. J Hepatol, 2023 Feb;78:333-342).This amino acid position is well conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Missense alterations in APC are not a common cause of disease (Spier I et al. Genet Med. 2024 Feb;26(2):100992). Based on the available evidence, the clinical significance of this variant remains unclear. (less)
|
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:
The p.V1125G variant (also known as c.3374T>G), located in coding exon 15 of the APC gene, results from a T to G substitution at nucleotide position 3374. The valine at codon 1125 is replaced by glycine, an amino acid with dissimilar properties. This variant was detected in 1 of 1292 individuals with biliary tract cancer and 2 of 37583 controls without a personal or family history of biliary tract cancer in Japan (Okawa Y et al. J Hepatol, 2023 Feb;78:333-342).This amino acid position is well conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Missense alterations in APC are not a common cause of disease (Spier I et al. Genet Med. 2024 Feb;26(2):100992). Based on the available evidence, the clinical significance of this variant remains unclear.
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| Hereditary cancer variants and homologous recombination deficiency in biliary tract cancer. | Okawa Y | Journal of hepatology | 2023 | PMID: 36243179 |
Text-mined citations for this variant ...
HelpRecord last updated Jan 13, 2025
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.