The p.G2610R variant (also known as c.7828G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 7828. The glycine at codon 2610 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
ClinVar Genomic variation as it relates to human health
NM_000038.6(APC):c.7828G>A (p.Gly2610Arg)
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.
(2)
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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
2
criteria provided, multiple submitters, no conflicts
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.7828G>A (p.Gly2610Arg)
Variation ID: 2106397 Accession: VCV002106397.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 5q22.2 5: 112843422 (GRCh38) [ NCBI UCSC ] 5: 112179119 (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 8, 2023 Feb 20, 2024 Apr 5, 2023 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_000038.6:c.7828G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000029.2:p.Gly2610Arg missense NM_000038.5:c.7828G>A NM_001127510.3:c.7828G>A NP_001120982.1:p.Gly2610Arg missense NM_001127511.3:c.7774G>A NP_001120983.2:p.Gly2592Arg missense NM_001354895.2:c.7828G>A NP_001341824.1:p.Gly2610Arg missense NM_001354896.2:c.7882G>A NP_001341825.1:p.Gly2628Arg missense NM_001354897.2:c.7858G>A NP_001341826.1:p.Gly2620Arg missense NM_001354898.2:c.7753G>A NP_001341827.1:p.Gly2585Arg missense NM_001354899.2:c.7744G>A NP_001341828.1:p.Gly2582Arg missense NM_001354900.2:c.7705G>A NP_001341829.1:p.Gly2569Arg missense NM_001354901.2:c.7651G>A NP_001341830.1:p.Gly2551Arg missense NM_001354902.2:c.7555G>A NP_001341831.1:p.Gly2519Arg missense NM_001354903.2:c.7525G>A NP_001341832.1:p.Gly2509Arg missense NM_001354904.2:c.7450G>A NP_001341833.1:p.Gly2484Arg missense NM_001354905.2:c.7348G>A NP_001341834.1:p.Gly2450Arg missense NM_001354906.2:c.6979G>A NP_001341835.1:p.Gly2327Arg missense NM_001407446.1:c.7912G>A NP_001394375.1:p.Gly2638Arg missense NM_001407447.1:c.7882G>A NP_001394376.1:p.Gly2628Arg missense NM_001407448.1:c.7882G>A NP_001394377.1:p.Gly2628Arg missense NM_001407449.1:c.7882G>A NP_001394378.1:p.Gly2628Arg missense NM_001407450.1:c.7828G>A NP_001394379.1:p.Gly2610Arg missense NM_001407451.1:c.7807G>A NP_001394380.1:p.Gly2603Arg missense NM_001407452.1:c.7798G>A NP_001394381.1:p.Gly2600Arg missense NM_001407453.1:c.7651G>A NP_001394382.1:p.Gly2551Arg missense NM_001407454.1:c.7579G>A NP_001394383.1:p.Gly2527Arg missense NM_001407455.1:c.7579G>A NP_001394384.1:p.Gly2527Arg missense NM_001407456.1:c.7579G>A NP_001394385.1:p.Gly2527Arg missense NM_001407457.1:c.7579G>A NP_001394386.1:p.Gly2527Arg missense NM_001407458.1:c.7525G>A NP_001394387.1:p.Gly2509Arg missense NM_001407459.1:c.7525G>A NP_001394388.1:p.Gly2509Arg missense NM_001407460.1:c.7525G>A NP_001394389.1:p.Gly2509Arg missense NM_001407467.1:c.7441G>A NP_001394396.1:p.Gly2481Arg missense NM_001407469.1:c.7441G>A NP_001394398.1:p.Gly2481Arg missense NM_001407470.1:c.6979G>A NP_001394399.1:p.Gly2327Arg missense NM_001407471.1:c.6676G>A NP_001394400.1:p.Gly2226Arg missense NM_001407472.1:c.6676G>A NP_001394401.1:p.Gly2226Arg missense NR_176365.1:n.7663G>A NR_176366.1:n.8082G>A NC_000005.10:g.112843422G>A NC_000005.9:g.112179119G>A NG_008481.4:g.155902G>A LRG_130:g.155902G>A LRG_130t1:c.7828G>A LRG_130p1:p.Gly2610Arg LRG_130t2:c.7828G>A LRG_130p2:p.Gly2610Arg LRG_130t3:c.7828G>A LRG_130p3:p.Gly2610Arg - Protein change
- G2327R, G2484R, G2527R, G2569R, G2600R, G2628R, G2638R, G2226R, G2582R, G2592R, G2603R, G2610R, G2519R, G2450R, G2481R, G2509R, G2551R, G2585R, G2620R
- Other names
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- Canonical SPDI
- NC_000005.10:112843421:G:A
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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 |
14965 | 15103 | |
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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Apr 5, 2023 | RCV003308437.1 | |
| Uncertain significance (1) |
criteria provided, single submitter
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Nov 17, 2021 | RCV004572580.2 |
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
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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
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
(Apr 05, 2023)
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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: SCV004005103.1
First in ClinVar: Jul 08, 2023 Last updated: Jul 08, 2023 |
Comment:
The p.G2610R variant (also known as c.7828G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide … (more)
The p.G2610R variant (also known as c.7828G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 7828. The glycine at codon 2610 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. (less)
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Uncertain significance
(Nov 17, 2021)
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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: SCV003322943.2
First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024 |
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant … (more)
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2610 of the APC protein (p.Gly2610Arg). (less)
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Comment:
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2610 of the APC protein (p.Gly2610Arg).
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.G2610R variant (also known as c.7828G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 7828. The glycine at codon 2610 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Comment:
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2610 of the APC protein (p.Gly2610Arg).
Citations for germline classification of this variant
Help| There 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 Nov 03, 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.