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NM_000038.6(APC):c.7504G>A (p.Gly2502Ser) AND Carcinoma of colon

Germline classification:
Benign (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001353410.9

Allele description [Variation Report for NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)]

NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.7504G>A (p.Gly2502Ser)
Other names:
p.G2502S:GGT>AGT; CCDS4107.1:c.7504G>A
HGVS:
  • NC_000005.10:g.112843098G>A
  • NG_008481.4:g.155578G>A
  • NM_000038.6:c.7504G>AMANE SELECT
  • NM_001127510.3:c.7504G>A
  • NM_001127511.3:c.7450G>A
  • NM_001354895.2:c.7504G>A
  • NM_001354896.2:c.7558G>A
  • NM_001354897.2:c.7534G>A
  • NM_001354898.2:c.7429G>A
  • NM_001354899.2:c.7420G>A
  • NM_001354900.2:c.7381G>A
  • NM_001354901.2:c.7327G>A
  • NM_001354902.2:c.7231G>A
  • NM_001354903.2:c.7201G>A
  • NM_001354904.2:c.7126G>A
  • NM_001354905.2:c.7024G>A
  • NM_001354906.2:c.6655G>A
  • NP_000029.2:p.Gly2502Ser
  • NP_000029.2:p.Gly2502Ser
  • NP_001120982.1:p.Gly2502Ser
  • NP_001120983.2:p.Gly2484Ser
  • NP_001341824.1:p.Gly2502Ser
  • NP_001341825.1:p.Gly2520Ser
  • NP_001341826.1:p.Gly2512Ser
  • NP_001341827.1:p.Gly2477Ser
  • NP_001341828.1:p.Gly2474Ser
  • NP_001341829.1:p.Gly2461Ser
  • NP_001341830.1:p.Gly2443Ser
  • NP_001341831.1:p.Gly2411Ser
  • NP_001341832.1:p.Gly2401Ser
  • NP_001341833.1:p.Gly2376Ser
  • NP_001341834.1:p.Gly2342Ser
  • NP_001341835.1:p.Gly2219Ser
  • LRG_130t1:c.7504G>A
  • LRG_130:g.155578G>A
  • LRG_130p1:p.Gly2502Ser
  • NC_000005.9:g.112178795G>A
  • NM_000038.4:c.7504G>A
  • NM_000038.5:c.7504G>A
  • NM_001127510.2:c.7504G>A
  • NM_001127511.2:c.7450G>A
  • P25054:p.Gly2502Ser
  • p.G2502S
Protein change:
G2219S
Links:
UniProtKB: P25054#VAR_005055; dbSNP: rs2229995
NCBI 1000 Genomes Browser:
rs2229995
Molecular consequence:
  • NM_000038.6:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.7450G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7504G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7558G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7534G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.7429G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.7420G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.7381G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.7327G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.7231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.7201G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.7126G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.7024G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6655G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Carcinoma of colon (CRC)
Synonyms:
Colonic carcinoma; Colon carcinoma
Identifiers:
MONDO: MONDO:0002032; MedGen: C0699790

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000591209Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Benignunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591209.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The p.Gly2502Ser variant was previously identified in the literature in 138 of 6866 proband chromosomes (frequency 0.020) from individuals with adenoma or colorectal cancer and in 157 of 8192 control chromosomes (frequency 0.019) from healthy individuals (Cleary 2008, Hadjisavvas 2006, Miyoshi 1992, Scott 2004, Tranah 2005, Wong 2010, Zhou 2004). This variant was also identified in the dbSNP (ID#rs2229995), HGMD, and LOVD databases, and was reported in several populations including the ESP Project with a frequency of 0.020 in European American alleles, the 1000 Genomes Project with a frequency of 0.010, and HapMap-CEU with a frequency of 0.032. The p.Gly2502 residue is not conserved through evolution and the variant (Ser) is found at this position in chicken and fruitfly, increasing the likelihood that this is a benign variant. In addition, Tranah (2005) found that this variant was not associated with risk of colorectal cancer or adenoma in men and women, and Zhou (2004) did not observe segregation of this variant with disease. In summary, based on the above information, this variant meets our laboratory's criteria to be classified as benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 26, 2024