NM_000038.6(APC):c.4420G>A (p.Ala1474Thr) AND APC-Associated Polyposis Disorders

Germline classification:: Likely benign (1 submission)
Last evaluated:: Nov 29, 2018
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:: RCV000321870.12

Allele description [Variation Report for NM_000038.6(APC):c.4420G>A (p.Ala1474Thr)]

NM_000038.6(APC):c.4420G>A (p.Ala1474Thr)

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.4420G>A (p.Ala1474Thr)

Other names:

p.A1474T:GCT>ACT; NM_000038.6(APC):c.4420G>A

HGVS:

NC_000005.10:g.112840014G>A
NG_008481.4:g.152494G>A
NM_000038.6:c.4420G>AMANE SELECT
NM_001127510.3:c.4420G>A
NM_001127511.3:c.4366G>A
NM_001354895.2:c.4420G>A
NM_001354896.2:c.4474G>A
NM_001354897.2:c.4450G>A
NM_001354898.2:c.4345G>A
NM_001354899.2:c.4336G>A
NM_001354900.2:c.4297G>A
NM_001354901.2:c.4243G>A
NM_001354902.2:c.4147G>A
NM_001354903.2:c.4117G>A
NM_001354904.2:c.4042G>A
NM_001354905.2:c.3940G>A
NM_001354906.2:c.3571G>A
NP_000029.2:p.Ala1474Thr
NP_001120982.1:p.Ala1474Thr
NP_001120983.2:p.Ala1456Thr
NP_001341824.1:p.Ala1474Thr
NP_001341825.1:p.Ala1492Thr
NP_001341826.1:p.Ala1484Thr
NP_001341827.1:p.Ala1449Thr
NP_001341828.1:p.Ala1446Thr
NP_001341829.1:p.Ala1433Thr
NP_001341830.1:p.Ala1415Thr
NP_001341831.1:p.Ala1383Thr
NP_001341832.1:p.Ala1373Thr
NP_001341833.1:p.Ala1348Thr
NP_001341834.1:p.Ala1314Thr
NP_001341835.1:p.Ala1191Thr
LRG_130t1:c.4420G>A
LRG_130:g.152494G>A
NC_000005.9:g.112175711G>A
NM_000038.4:c.4420G>A
NM_000038.5:c.4420G>A
NM_001127510.2:c.4420G>A
p.A1474T

Protein change:

A1191T

Links:

dbSNP: rs139387758

Molecular consequence:

NM_000038.6:c.4420G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.4420G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.4366G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.4420G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.4474G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.4450G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.4345G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.4336G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.4297G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.4243G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.4147G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.4117G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.4042G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.3940G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.3571G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: APC-Associated Polyposis Disorders
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000452012	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Nov 29, 2018)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 24055113, 21859464, 2472832, 24728327, 25637381, 26332594, 24861525, 18199528 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000452012

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Nov 29, 2018)

germline

clinical testing

PubMed (8)
[See all records that cite these PMIDs]

Citation Link

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

Actionable, pathogenic incidental findings in 1,000 participants' exomes.

Dorschner MO, Amendola LM, Turner EH, Robertson PD, Shirts BH, Gallego CJ, Bennett RL, Jones KL, Tokita MJ, Bennett JT, Kim JH, Rosenthal EA, Kim DS; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project, Tabor HK, Bamshad MJ, Motulsky AG, Scott CR, Pritchard CC, Walsh T, Burke W, Raskind WH, et al.

Am J Hum Genet. 2013 Oct 3;93(4):631-40. doi: 10.1016/j.ajhg.2013.08.006. Epub 2013 Sep 19.

PubMed [citation]

PMID:: 24055113
PMCID:: PMC3791261

Messing up disorder: how do missense mutations in the tumor suppressor protein APC lead to cancer?

Minde DP, Anvarian Z, Rüdiger SG, Maurice MM.

Mol Cancer. 2011 Aug 22;10:101. doi: 10.1186/1476-4598-10-101. Review.

PubMed [citation]

PMID:: 21859464
PMCID:: PMC3170638

See all PubMed Citations (8)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000452012.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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 20, 2026

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