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NM_000038.6(APC):c.7739C>T (p.Ser2580Phe) AND Familial adenomatous polyposis 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 23, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003535922.1

Allele description

NM_000038.6(APC):c.7739C>T (p.Ser2580Phe)

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.7739C>T (p.Ser2580Phe)
HGVS:
  • NC_000005.10:g.112843333C>T
  • NG_008481.4:g.155813C>T
  • NM_000038.6:c.7739C>TMANE SELECT
  • NM_001127510.3:c.7739C>T
  • NM_001127511.3:c.7685C>T
  • NM_001354895.2:c.7739C>T
  • NM_001354896.2:c.7793C>T
  • NM_001354897.2:c.7769C>T
  • NM_001354898.2:c.7664C>T
  • NM_001354899.2:c.7655C>T
  • NM_001354900.2:c.7616C>T
  • NM_001354901.2:c.7562C>T
  • NM_001354902.2:c.7466C>T
  • NM_001354903.2:c.7436C>T
  • NM_001354904.2:c.7361C>T
  • NM_001354905.2:c.7259C>T
  • NM_001354906.2:c.6890C>T
  • NP_000029.2:p.Ser2580Phe
  • NP_001120982.1:p.Ser2580Phe
  • NP_001120983.2:p.Ser2562Phe
  • NP_001341824.1:p.Ser2580Phe
  • NP_001341825.1:p.Ser2598Phe
  • NP_001341826.1:p.Ser2590Phe
  • NP_001341827.1:p.Ser2555Phe
  • NP_001341828.1:p.Ser2552Phe
  • NP_001341829.1:p.Ser2539Phe
  • NP_001341830.1:p.Ser2521Phe
  • NP_001341831.1:p.Ser2489Phe
  • NP_001341832.1:p.Ser2479Phe
  • NP_001341833.1:p.Ser2454Phe
  • NP_001341834.1:p.Ser2420Phe
  • NP_001341835.1:p.Ser2297Phe
  • LRG_130:g.155813C>T
  • NC_000005.9:g.112179030C>T
  • NM_000038.5:c.7739C>T
Protein change:
S2297F
Links:
dbSNP: rs1012830859
NCBI 1000 Genomes Browser:
rs1012830859
Molecular consequence:
  • NM_000038.6:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.7685C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7739C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7793C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7769C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.7664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.7655C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.7616C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.7562C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.7466C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.7436C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.7361C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.7259C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6890C>T - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000941534Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 23, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Details of each submission

From Invitae, SCV000941534.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with APC-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with phenylalanine at codon 2580 of the APC protein (p.Ser2580Phe). The serine residue is highly conserved and there is a large physicochemical difference between serine and phenylalanine.

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

Last Updated: Jun 2, 2024