NM_000038.6(APC):c.5009C>T (p.Ala1670Val) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Oct 24, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000586353.45

Allele description [Variation Report for NM_000038.6(APC):c.5009C>T (p.Ala1670Val)]

NM_000038.6(APC):c.5009C>T (p.Ala1670Val)

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.5009C>T (p.Ala1670Val)

HGVS:

NC_000005.10:g.112840603C>T
NG_008481.4:g.153083C>T
NM_000038.6:c.5009C>TMANE SELECT
NM_001127510.3:c.5009C>T
NM_001127511.3:c.4955C>T
NM_001354895.2:c.5009C>T
NM_001354896.2:c.5063C>T
NM_001354897.2:c.5039C>T
NM_001354898.2:c.4934C>T
NM_001354899.2:c.4925C>T
NM_001354900.2:c.4886C>T
NM_001354901.2:c.4832C>T
NM_001354902.2:c.4736C>T
NM_001354903.2:c.4706C>T
NM_001354904.2:c.4631C>T
NM_001354905.2:c.4529C>T
NM_001354906.2:c.4160C>T
NP_000029.2:p.Ala1670Val
NP_001120982.1:p.Ala1670Val
NP_001120983.2:p.Ala1652Val
NP_001341824.1:p.Ala1670Val
NP_001341825.1:p.Ala1688Val
NP_001341826.1:p.Ala1680Val
NP_001341827.1:p.Ala1645Val
NP_001341828.1:p.Ala1642Val
NP_001341829.1:p.Ala1629Val
NP_001341830.1:p.Ala1611Val
NP_001341831.1:p.Ala1579Val
NP_001341832.1:p.Ala1569Val
NP_001341833.1:p.Ala1544Val
NP_001341834.1:p.Ala1510Val
NP_001341835.1:p.Ala1387Val
LRG_130t1:c.5009C>T
LRG_130:g.153083C>T
NC_000005.9:g.112176300C>T
NM_000038.4:c.5009C>T
NM_000038.5:c.5009C>T
p.A1670V

Protein change:

A1387V

Links:

dbSNP: rs202228932

NCBI 1000 Genomes Browser:

rs202228932

Molecular consequence:

NM_000038.6:c.5009C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.5009C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.4955C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.5009C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.5063C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.5039C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.4934C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.4925C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.4886C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.4832C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.4736C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.4706C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.4631C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.4529C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.4160C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000292460	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Nov 20, 2020)	germline	clinical testing	Citation Link,
SCV000691756	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 6, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 26580448, 28502729, 28944238, 30680046, 25741868
SCV000805418	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 20, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001133340	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Oct 24, 2022)	unknown	clinical testing	PubMed (7) [See all records that cite these PMIDs] 26580448, 27705013, 28502729, 28944238, 26207792, 30680046, 26467025
SCV001154470	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Jan 1, 2019)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	13	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Germline Mutations in Predisposition Genes in Pediatric Cancer.

Zhang J, Walsh MF, Wu G, Edmonson MN, Gruber TA, Easton J, Hedges D, Ma X, Zhou X, Yergeau DA, Wilkinson MR, Vadodaria B, Chen X, McGee RB, Hines-Dowell S, Nuccio R, Quinn E, Shurtleff SA, Rusch M, Patel A, Becksfort JB, Wang S, et al.

N Engl J Med. 2015 Dec 10;373(24):2336-2346. doi: 10.1056/NEJMoa1508054. Epub 2015 Nov 18.

PubMed [citation]

PMID:: 26580448
PMCID:: PMC4734119

See all PubMed Citations (8)

Details of each submission

From GeneDx, SCV000292460.10

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

Description

This variant is associated with the following publications: (PMID: 25991819, 26336887, 26207792, 28502729, 27705013, 28944238, 30680046)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000691756.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	13	not provided	not provided	clinical testing	PubMed (5)

Description

BS1

#	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		13	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000805418.1

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001133340.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV001154470.27

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

Last Updated: Nov 24, 2024

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