NM_000038.6(APC):c.5982C>A (p.Asp1994Glu) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 20, 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:: RCV003742749.1

Allele description

NM_000038.6(APC):c.5982C>A (p.Asp1994Glu)

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.5982C>A (p.Asp1994Glu)

HGVS:

NC_000005.10:g.112841576C>A
NG_008481.4:g.154056C>A
NM_000038.6:c.5982C>AMANE SELECT
NM_001127510.3:c.5982C>A
NM_001127511.3:c.5928C>A
NM_001354895.2:c.5982C>A
NM_001354896.2:c.6036C>A
NM_001354897.2:c.6012C>A
NM_001354898.2:c.5907C>A
NM_001354899.2:c.5898C>A
NM_001354900.2:c.5859C>A
NM_001354901.2:c.5805C>A
NM_001354902.2:c.5709C>A
NM_001354903.2:c.5679C>A
NM_001354904.2:c.5604C>A
NM_001354905.2:c.5502C>A
NM_001354906.2:c.5133C>A
NP_000029.2:p.Asp1994Glu
NP_001120982.1:p.Asp1994Glu
NP_001120983.2:p.Asp1976Glu
NP_001341824.1:p.Asp1994Glu
NP_001341825.1:p.Asp2012Glu
NP_001341826.1:p.Asp2004Glu
NP_001341827.1:p.Asp1969Glu
NP_001341828.1:p.Asp1966Glu
NP_001341829.1:p.Asp1953Glu
NP_001341830.1:p.Asp1935Glu
NP_001341831.1:p.Asp1903Glu
NP_001341832.1:p.Asp1893Glu
NP_001341833.1:p.Asp1868Glu
NP_001341834.1:p.Asp1834Glu
NP_001341835.1:p.Asp1711Glu
LRG_130:g.154056C>A
NC_000005.9:g.112177273C>A
NM_000038.5:c.5982C>A

Protein change:

D1711E

Links:

dbSNP: rs372852823

NCBI 1000 Genomes Browser:

rs372852823

Molecular consequence:

NM_000038.6:c.5982C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.5982C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.5928C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.5982C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.6036C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.6012C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.5907C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.5898C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.5859C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.5805C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.5709C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.5679C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.5604C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.5502C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.5133C>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
SCV000647618	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 20, 2017)	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

SCV000647618

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 20, 2017)

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, SCV000647618.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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 a APC-related disease. This sequence change replaces aspartic acid with glutamic acid at codon 1994 of the APC protein (p.Asp1994Glu). The aspartic acid residue is moderately conserved and there is a small physicochemical difference between aspartic acid and glutamic acid. In summary, this variant is a novel missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies.

#	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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