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NM_000038.6(APC):c.8389A>G (p.Ser2797Gly) AND Familial adenomatous polyposis 1

Germline classification:
Conflicting classifications of pathogenicity (4 submissions)
Last evaluated:
Jan 28, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000198030.28

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)

Name:
Familial adenomatous polyposis 1 (FAP1)
Synonyms:
POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:
MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000254049Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely benign
(Jan 28, 2024)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000488295Counsyl
criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))
Uncertain significance
(Feb 19, 2016)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV000838162Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Uncertain significance
(Jul 2, 2018)
unknownclinical testing

Citation Link,

SCV004018764Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))
Uncertain significance
(Feb 21, 2023)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9..

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000254049.13

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Counsyl, SCV000488295.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV000838162.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Myriad Genetics, Inc., SCV004018764.1

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

Description

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

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

Last Updated: Jan 19, 2025