NM_000038.6(APC):c.7763A>G (p.Asp2588Gly) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 30, 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:: RCV003744553.1

Allele description

NM_000038.6(APC):c.7763A>G (p.Asp2588Gly)

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.7763A>G (p.Asp2588Gly)

HGVS:

NC_000005.10:g.112843357A>G
NG_008481.4:g.155837A>G
NM_000038.6:c.7763A>GMANE SELECT
NM_001127510.3:c.7763A>G
NM_001127511.3:c.7709A>G
NM_001354895.2:c.7763A>G
NM_001354896.2:c.7817A>G
NM_001354897.2:c.7793A>G
NM_001354898.2:c.7688A>G
NM_001354899.2:c.7679A>G
NM_001354900.2:c.7640A>G
NM_001354901.2:c.7586A>G
NM_001354902.2:c.7490A>G
NM_001354903.2:c.7460A>G
NM_001354904.2:c.7385A>G
NM_001354905.2:c.7283A>G
NM_001354906.2:c.6914A>G
NP_000029.2:p.Asp2588Gly
NP_001120982.1:p.Asp2588Gly
NP_001120983.2:p.Asp2570Gly
NP_001341824.1:p.Asp2588Gly
NP_001341825.1:p.Asp2606Gly
NP_001341826.1:p.Asp2598Gly
NP_001341827.1:p.Asp2563Gly
NP_001341828.1:p.Asp2560Gly
NP_001341829.1:p.Asp2547Gly
NP_001341830.1:p.Asp2529Gly
NP_001341831.1:p.Asp2497Gly
NP_001341832.1:p.Asp2487Gly
NP_001341833.1:p.Asp2462Gly
NP_001341834.1:p.Asp2428Gly
NP_001341835.1:p.Asp2305Gly
LRG_130:g.155837A>G
NC_000005.9:g.112179054A>G
NM_000038.5:c.7763A>G

Protein change:

D2305G

Links:

dbSNP: rs1554088648

NCBI 1000 Genomes Browser:

rs1554088648

Molecular consequence:

NM_000038.6:c.7763A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7763A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7709A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7763A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7817A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7793A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7688A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7679A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7640A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7586A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7490A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7460A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7385A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7283A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6914A>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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003348340	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 30, 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

SCV003348340

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 30, 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, SCV003348340.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. 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. ClinVar contains an entry for this variant (Variation ID: 482420). This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with glycine, which is neutral and non-polar, at codon 2588 of the APC protein (p.Asp2588Gly).

#	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 9, 2024

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