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NM_000038.6(APC):c.5009C>T (p.Ala1670Val) AND Hereditary cancer-predisposing syndrome

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Oct 31, 2023
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:
RCV000128987.19

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]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000172877Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)
Likely benign
(Dec 28, 2018)
germlineclinical testing

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

Citation Link,

SCV000910625Color Diagnostics, LLC DBA Color Health
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Jun 24, 2016)
germlineclinical testing

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

SCV002534954Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)
Likely benign
(Aug 10, 2021)
germlinecuration

PubMed (6)
[See all records that cite these PMIDs]

Citation Link,

SCV004227996Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Oct 31, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Diagnostic yield and clinical utility of a comprehensive gene panel for hereditary tumor syndromes.

Henn J, Spier I, Adam RS, Holzapfel S, Uhlhaas S, Kayser K, Plotz G, Peters S, Aretz S.

Hered Cancer Clin Pract. 2019;17:5. doi: 10.1186/s13053-018-0102-4.

PubMed [citation]
PMID:
30680046
PMCID:
PMC6343270

Targeted sequencing of 36 known or putative colorectal cancer susceptibility genes.

DeRycke MS, Gunawardena S, Balcom JR, Pickart AM, Waltman LA, French AJ, McDonnell S, Riska SM, Fogarty ZC, Larson MC, Middha S, Eckloff BW, Asmann YW, Ferber MJ, Haile RW, Gallinger S, Clendenning M, Rosty C, Win AK, Buchanan DD, Hopper JL, Newcomb PA, et al.

Mol Genet Genomic Med. 2017 Sep;5(5):553-569. doi: 10.1002/mgg3.317.

PubMed [citation]
PMID:
28944238
PMCID:
PMC5606870
See all PubMed Citations (7)

Details of each submission

From Ambry Genetics, SCV000172877.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Color Diagnostics, LLC DBA Color Health, SCV000910625.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Sema4, Sema4, SCV002534954.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (6)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., SCV004227996.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 24, 2024