NM_000038.6(APC):c.5066C>A (p.Thr1689Asn) AND Familial adenomatous polyposis 1

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 28, 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:: RCV002526661.10

Allele description [Variation Report for NM_000038.6(APC):c.5066C>A (p.Thr1689Asn)]

NM_000038.6(APC):c.5066C>A (p.Thr1689Asn)

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.5066C>A (p.Thr1689Asn)

HGVS:

NC_000005.10:g.112840660C>A
NG_008481.4:g.153140C>A
NM_000038.6:c.5066C>AMANE SELECT
NM_001127510.3:c.5066C>A
NM_001127511.3:c.5012C>A
NM_001354895.2:c.5066C>A
NM_001354896.2:c.5120C>A
NM_001354897.2:c.5096C>A
NM_001354898.2:c.4991C>A
NM_001354899.2:c.4982C>A
NM_001354900.2:c.4943C>A
NM_001354901.2:c.4889C>A
NM_001354902.2:c.4793C>A
NM_001354903.2:c.4763C>A
NM_001354904.2:c.4688C>A
NM_001354905.2:c.4586C>A
NM_001354906.2:c.4217C>A
NP_000029.2:p.Thr1689Asn
NP_001120982.1:p.Thr1689Asn
NP_001120983.2:p.Thr1671Asn
NP_001341824.1:p.Thr1689Asn
NP_001341825.1:p.Thr1707Asn
NP_001341826.1:p.Thr1699Asn
NP_001341827.1:p.Thr1664Asn
NP_001341828.1:p.Thr1661Asn
NP_001341829.1:p.Thr1648Asn
NP_001341830.1:p.Thr1630Asn
NP_001341831.1:p.Thr1598Asn
NP_001341832.1:p.Thr1588Asn
NP_001341833.1:p.Thr1563Asn
NP_001341834.1:p.Thr1529Asn
NP_001341835.1:p.Thr1406Asn
LRG_130:g.153140C>A
NC_000005.9:g.112176357C>A
NM_000038.5:c.5066C>A

Protein change:

T1406N

Links:

dbSNP: rs551084068

NCBI 1000 Genomes Browser:

rs551084068

Molecular consequence:

NM_000038.6:c.5066C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.5066C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.5012C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.5066C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.5120C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.5096C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.4991C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.4982C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.4943C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.4889C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.4793C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.4763C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.4688C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.4586C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.4217C>A - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002189372	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 28, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004203991	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 5, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002189372

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 28, 2023)

germline

clinical testing

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

SCV004203991

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 5, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	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

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Invitae, SCV002189372.3

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

Description

This sequence change replaces threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 1689 of the APC protein (p.Thr1689Asn). This variant is present in population databases (rs551084068, 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: 423347). 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. 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.

#	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 Baylor Genetics, SCV004203991.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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