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NM_000038.6(APC):c.7664C>T (p.Ser2555Leu) AND Familial adenomatous polyposis 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 8, 2017
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:
RCV003742792.1

Allele description

NM_000038.6(APC):c.7664C>T (p.Ser2555Leu)

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.7664C>T (p.Ser2555Leu)
HGVS:
  • NC_000005.10:g.112843258C>T
  • NG_008481.4:g.155738C>T
  • NM_000038.6:c.7664C>TMANE SELECT
  • NM_001127510.3:c.7664C>T
  • NM_001127511.3:c.7610C>T
  • NM_001354895.2:c.7664C>T
  • NM_001354896.2:c.7718C>T
  • NM_001354897.2:c.7694C>T
  • NM_001354898.2:c.7589C>T
  • NM_001354899.2:c.7580C>T
  • NM_001354900.2:c.7541C>T
  • NM_001354901.2:c.7487C>T
  • NM_001354902.2:c.7391C>T
  • NM_001354903.2:c.7361C>T
  • NM_001354904.2:c.7286C>T
  • NM_001354905.2:c.7184C>T
  • NM_001354906.2:c.6815C>T
  • NP_000029.2:p.Ser2555Leu
  • NP_001120982.1:p.Ser2555Leu
  • NP_001120983.2:p.Ser2537Leu
  • NP_001341824.1:p.Ser2555Leu
  • NP_001341825.1:p.Ser2573Leu
  • NP_001341826.1:p.Ser2565Leu
  • NP_001341827.1:p.Ser2530Leu
  • NP_001341828.1:p.Ser2527Leu
  • NP_001341829.1:p.Ser2514Leu
  • NP_001341830.1:p.Ser2496Leu
  • NP_001341831.1:p.Ser2464Leu
  • NP_001341832.1:p.Ser2454Leu
  • NP_001341833.1:p.Ser2429Leu
  • NP_001341834.1:p.Ser2395Leu
  • NP_001341835.1:p.Ser2272Leu
  • LRG_130:g.155738C>T
  • NC_000005.9:g.112178955C>T
  • NM_000038.5:c.7664C>T
Protein change:
S2272L
Links:
dbSNP: rs1554088582
NCBI 1000 Genomes Browser:
rs1554088582
Molecular consequence:
  • NM_000038.6:c.7664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.7610C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7664C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7718C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7694C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.7589C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.7580C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.7541C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.7487C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.7391C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.7361C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.7286C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.7184C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6815C>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
SCV000647724Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 8, 2017) 		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, SCV000647724.4

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

Description

This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with an APC-related disease. This sequence change replaces serine with leucine at codon 2555 of the APC protein (p.Ser2555Leu). The serine residue is highly conserved and there is a large physicochemical difference between serine and leucine. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

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

Last Updated: Jun 9, 2024