NM_000038.6(APC):c.8389A>G (p.Ser2797Gly) AND not provided

Germline classification:: Uncertain significance (6 submissions)
Last evaluated:: Jun 9, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000656753.23

Allele description [Variation Report for NM_000038.6(APC):c.8389A>G (p.Ser2797Gly)]

NM_000038.6(APC):c.8389A>G (p.Ser2797Gly)

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.8389A>G (p.Ser2797Gly)

HGVS:

NC_000005.10:g.112843983A>G
NG_008481.4:g.156463A>G
NM_000038.6:c.8389A>GMANE SELECT
NM_001127510.3:c.8389A>G
NM_001127511.3:c.8335A>G
NM_001354895.2:c.8389A>G
NM_001354896.2:c.8443A>G
NM_001354897.2:c.8419A>G
NM_001354898.2:c.8314A>G
NM_001354899.2:c.8305A>G
NM_001354900.2:c.8266A>G
NM_001354901.2:c.8212A>G
NM_001354902.2:c.8116A>G
NM_001354903.2:c.8086A>G
NM_001354904.2:c.8011A>G
NM_001354905.2:c.7909A>G
NM_001354906.2:c.7540A>G
NP_000029.2:p.Ser2797Gly
NP_001120982.1:p.Ser2797Gly
NP_001120983.2:p.Ser2779Gly
NP_001341824.1:p.Ser2797Gly
NP_001341825.1:p.Ser2815Gly
NP_001341826.1:p.Ser2807Gly
NP_001341827.1:p.Ser2772Gly
NP_001341828.1:p.Ser2769Gly
NP_001341829.1:p.Ser2756Gly
NP_001341830.1:p.Ser2738Gly
NP_001341831.1:p.Ser2706Gly
NP_001341832.1:p.Ser2696Gly
NP_001341833.1:p.Ser2671Gly
NP_001341834.1:p.Ser2637Gly
NP_001341835.1:p.Ser2514Gly
LRG_130:g.156463A>G
NC_000005.9:g.112179680A>G
NM_000038.5:c.8389A>G
p.S2797G

Protein change:

S2514G

Links:

dbSNP: rs147287751

NCBI 1000 Genomes Browser:

rs147287751

Molecular consequence:

NM_000038.6:c.8389A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.8389A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.8335A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.8389A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.8443A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.8419A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.8314A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.8305A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.8266A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.8212A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.8116A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.8086A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.8011A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7909A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.7540A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000292468	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 9, 2023)	germline	clinical testing	Citation Link,
SCV000600167	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Apr 18, 2019)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 25186627, 28135145, 28608266, 26467025
SCV000805481	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 15, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001918221	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001954650	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001979842	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Frequency of mutations in individuals with breast cancer referred for BRCA1 and BRCA2 testing using next-generation sequencing with a 25-gene panel.

Tung N, Battelli C, Allen B, Kaldate R, Bhatnagar S, Bowles K, Timms K, Garber JE, Herold C, Ellisen L, Krejdovsky J, DeLeonardis K, Sedgwick K, Soltis K, Roa B, Wenstrup RJ, Hartman AR.

Cancer. 2015 Jan 1;121(1):25-33. doi: 10.1002/cncr.29010. Epub 2014 Sep 3.

PubMed [citation]

PMID:: 25186627

Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer.

Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, Ukaegbu CI, Brais LK, McNamara PG, Mayer RJ, Schrag D, Meyerhardt JA, Ng K, Kidd J, Singh N, Hartman AR, Wenstrup RJ, Syngal S.

J Clin Oncol. 2017 Apr 1;35(10):1086-1095. doi: 10.1200/JCO.2016.71.0012. Epub 2017 Jan 30.

PubMed [citation]

PMID:: 28135145
PMCID:: PMC5455355

See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000292468.14

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with colorectal cancer, colon polyp(s), and/or breast cancer (Tung et al., 2015; Jelsig et al., 2016; Dominguez-Valentin et al., 2017; Yurgelun et al., 2017; Guindalini et al., 2022); This variant is associated with the following publications: (PMID: 25186627, 28608266, 28135145, 16454848, 26580448, 27146957, 30122538, 35264596, 18199528)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000600167.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000805481.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001918221.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001954650.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001979842.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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