NM_000038.6(APC):c.7798C>G (p.Gln2600Glu) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 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:: RCV003537459.1

Allele description

NM_000038.6(APC):c.7798C>G (p.Gln2600Glu)

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.7798C>G (p.Gln2600Glu)

HGVS:

NC_000005.10:g.112843392C>G
NG_008481.4:g.155872C>G
NM_000038.6:c.7798C>GMANE SELECT
NM_001127510.3:c.7798C>G
NM_001127511.3:c.7744C>G
NM_001354895.2:c.7798C>G
NM_001354896.2:c.7852C>G
NM_001354897.2:c.7828C>G
NM_001354898.2:c.7723C>G
NM_001354899.2:c.7714C>G
NM_001354900.2:c.7675C>G
NM_001354901.2:c.7621C>G
NM_001354902.2:c.7525C>G
NM_001354903.2:c.7495C>G
NM_001354904.2:c.7420C>G
NM_001354905.2:c.7318C>G
NM_001354906.2:c.6949C>G
NP_000029.2:p.Gln2600Glu
NP_001120982.1:p.Gln2600Glu
NP_001120983.2:p.Gln2582Glu
NP_001341824.1:p.Gln2600Glu
NP_001341825.1:p.Gln2618Glu
NP_001341826.1:p.Gln2610Glu
NP_001341827.1:p.Gln2575Glu
NP_001341828.1:p.Gln2572Glu
NP_001341829.1:p.Gln2559Glu
NP_001341830.1:p.Gln2541Glu
NP_001341831.1:p.Gln2509Glu
NP_001341832.1:p.Gln2499Glu
NP_001341833.1:p.Gln2474Glu
NP_001341834.1:p.Gln2440Glu
NP_001341835.1:p.Gln2317Glu
LRG_130:g.155872C>G
NC_000005.9:g.112179089C>G
NM_000038.5:c.7798C>G

Protein change:

Q2317E

Links:

dbSNP: rs1766569773

NCBI 1000 Genomes Browser:

rs1766569773

Molecular consequence:

NM_000038.6:c.7798C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7798C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7744C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7798C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7852C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7828C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7723C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7714C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7675C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7621C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7525C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7495C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7420C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7318C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6949C>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

Recent activity

Clear Turn Off Turn On

Chain N, Chaperonin GroEL
Chain N, Chaperonin GroEL
gi|2753172369|pdb|8QXV|N

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001231212	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2023)	germline	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

SCV001231212

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2023)

germline

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	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001231212.5

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

Description

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. This sequence change replaces glutamine, which is neutral and polar, with glutamic acid, which is acidic and polar, at codon 2600 of the APC protein (p.Gln2600Glu). This variant is not present in population databases (gnomAD no frequency). 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: 859980). 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

Last Updated: Jun 2, 2024

ClinVar

Relating variation to medicine