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NM_000038.6(APC):c.7204A>T (p.Asn2402Tyr) AND Familial adenomatous polyposis 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 1, 2023
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:
RCV003764828.2

Allele description [Variation Report for NM_000038.6(APC):c.7204A>T (p.Asn2402Tyr)]

NM_000038.6(APC):c.7204A>T (p.Asn2402Tyr)

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.7204A>T (p.Asn2402Tyr)
HGVS:
  • NC_000005.10:g.112842798A>T
  • NG_008481.4:g.155278A>T
  • NM_000038.6:c.7204A>TMANE SELECT
  • NM_001127510.3:c.7204A>T
  • NM_001127511.3:c.7150A>T
  • NM_001354895.2:c.7204A>T
  • NM_001354896.2:c.7258A>T
  • NM_001354897.2:c.7234A>T
  • NM_001354898.2:c.7129A>T
  • NM_001354899.2:c.7120A>T
  • NM_001354900.2:c.7081A>T
  • NM_001354901.2:c.7027A>T
  • NM_001354902.2:c.6931A>T
  • NM_001354903.2:c.6901A>T
  • NM_001354904.2:c.6826A>T
  • NM_001354905.2:c.6724A>T
  • NM_001354906.2:c.6355A>T
  • NP_000029.2:p.Asn2402Tyr
  • NP_001120982.1:p.Asn2402Tyr
  • NP_001120983.2:p.Asn2384Tyr
  • NP_001341824.1:p.Asn2402Tyr
  • NP_001341825.1:p.Asn2420Tyr
  • NP_001341826.1:p.Asn2412Tyr
  • NP_001341827.1:p.Asn2377Tyr
  • NP_001341828.1:p.Asn2374Tyr
  • NP_001341829.1:p.Asn2361Tyr
  • NP_001341830.1:p.Asn2343Tyr
  • NP_001341831.1:p.Asn2311Tyr
  • NP_001341832.1:p.Asn2301Tyr
  • NP_001341833.1:p.Asn2276Tyr
  • NP_001341834.1:p.Asn2242Tyr
  • NP_001341835.1:p.Asn2119Tyr
  • LRG_130:g.155278A>T
  • NC_000005.9:g.112178495A>T
  • NM_000038.5:c.7204A>T
Protein change:
N2119Y
Links:
dbSNP: rs587780550
NCBI 1000 Genomes Browser:
rs587780550
Molecular consequence:
  • NM_000038.6:c.7204A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7204A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.7150A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7204A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7258A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7234A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.7129A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.7120A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.7081A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.7027A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.6931A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.6901A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.6826A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.6724A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6355A>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
SCV000153944Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Dec 1, 2023) 		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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000153944.4

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

Description

This sequence change replaces asparagine, which is neutral and polar, with tyrosine, which is neutral and polar, at codon 2402 of the APC protein (p.Asn2402Tyr). This variant is present in population databases (rs587780550, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 132747). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt APC protein function with a negative predictive value of 95%. 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.

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

Last Updated: Nov 3, 2024