NM_000038.6(APC):c.4420G>A (p.Ala1474Thr) AND not specified

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: Apr 25, 2017
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:: RCV000120040.23

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)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000084173	ITMI	no classification provided	not provided	germline	reference population	PubMed (1) [See all records that cite this PMID]
SCV000602521	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Likely benign (Oct 27, 2016)	germline	clinical testing	Citation Link,
SCV000805409	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Apr 25, 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

SCV000084173

ITMI

no classification provided

not provided

germline

reference population

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

SCV000602521

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Likely benign
(Oct 27, 2016)

germline

clinical testing

Citation Link,

SCV000805409

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Apr 25, 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
African	germline	unknown	not provided	not provided	not provided	43	not provided	reference population
African_European	germline	unknown	not provided	not provided	not provided	46	not provided	reference population
Central_Asian	germline	unknown	not provided	not provided	not provided	50	not provided	reference population
East_Asian	germline	unknown	not provided	not provided	not provided	62	not provided	reference population
European	germline	unknown	not provided	not provided	not provided	331	not provided	reference population
Hispanic	germline	unknown	not provided	not provided	not provided	118	not provided	reference population
Whole_cohort	germline	unknown	not provided	not provided	not provided	681	not provided	reference population

Citations

PubMed

Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing.

Bodian DL, McCutcheon JN, Kothiyal P, Huddleston KC, Iyer RK, Vockley JG, Niederhuber JE.

PLoS One. 2014;9(4):e94554. doi: 10.1371/journal.pone.0094554.

PubMed [citation]

PMID:: 24728327
PMCID:: PMC3984285

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 ITMI, SCV000084173.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	African	not provided	not provided	not provided	reference population	PubMed (1)
2	African_European	not provided	not provided	not provided	reference population	PubMed (1)
3	Central_Asian	not provided	not provided	not provided	reference population	PubMed (1)
4	East_Asian	not provided	not provided	not provided	reference population	PubMed (1)
5	European	not provided	not provided	not provided	reference population	PubMed (1)
6	Hispanic	not provided	not provided	not provided	reference population	PubMed (1)
7	Whole_cohort	not provided	not provided	not provided	reference population	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	43	not provided	discovery		not provided	0.0465	not provided	not provided
2	germline	unknown	46	not provided	discovery		not provided	0.0109	not provided	not provided
3	germline	unknown	50	not provided	discovery		not provided	0	not provided	not provided
4	germline	unknown	62	not provided	discovery		not provided	0	not provided	not provided
5	germline	unknown	331	not provided	discovery		not provided	0	not provided	not provided
6	germline	unknown	118	not provided	discovery		not provided	0	not provided	not provided
7	germline	unknown	681	not provided	discovery		not provided	0.0037	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000602521.1

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

#	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 PreventionGenetics, part of Exact Sciences, SCV000805409.1

#	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	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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