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NM_000038.6(APC):c.7036C>T (p.Pro2346Ser) AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:
Jul 1, 2024
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:
RCV000034397.40

Allele description [Variation Report for NM_000038.6(APC):c.7036C>T (p.Pro2346Ser)]

NM_000038.6(APC):c.7036C>T (p.Pro2346Ser)

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.7036C>T (p.Pro2346Ser)
Other names:
p.P2346S:CCA>TCA
HGVS:
  • NC_000005.10:g.112842630C>T
  • NG_008481.4:g.155110C>T
  • NM_000038.6:c.7036C>TMANE SELECT
  • NM_001127510.3:c.7036C>T
  • NM_001127511.3:c.6982C>T
  • NM_001354895.2:c.7036C>T
  • NM_001354896.2:c.7090C>T
  • NM_001354897.2:c.7066C>T
  • NM_001354898.2:c.6961C>T
  • NM_001354899.2:c.6952C>T
  • NM_001354900.2:c.6913C>T
  • NM_001354901.2:c.6859C>T
  • NM_001354902.2:c.6763C>T
  • NM_001354903.2:c.6733C>T
  • NM_001354904.2:c.6658C>T
  • NM_001354905.2:c.6556C>T
  • NM_001354906.2:c.6187C>T
  • NP_000029.2:p.Pro2346Ser
  • NP_001120982.1:p.Pro2346Ser
  • NP_001120983.2:p.Pro2328Ser
  • NP_001341824.1:p.Pro2346Ser
  • NP_001341825.1:p.Pro2364Ser
  • NP_001341826.1:p.Pro2356Ser
  • NP_001341827.1:p.Pro2321Ser
  • NP_001341828.1:p.Pro2318Ser
  • NP_001341829.1:p.Pro2305Ser
  • NP_001341830.1:p.Pro2287Ser
  • NP_001341831.1:p.Pro2255Ser
  • NP_001341832.1:p.Pro2245Ser
  • NP_001341833.1:p.Pro2220Ser
  • NP_001341834.1:p.Pro2186Ser
  • NP_001341835.1:p.Pro2063Ser
  • LRG_130t1:c.7036C>T
  • LRG_130:g.155110C>T
  • NC_000005.9:g.112178327C>T
  • NM_000038.4:c.7036C>T
  • NM_000038.5:c.7036C>T
  • p.P2346S
Protein change:
P2063S
Links:
dbSNP: rs200756935
NCBI 1000 Genomes Browser:
rs200756935
Molecular consequence:
  • NM_000038.6:c.7036C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127510.3:c.7036C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127511.3:c.6982C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354895.2:c.7036C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354896.2:c.7090C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354897.2:c.7066C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354898.2:c.6961C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354899.2:c.6952C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354900.2:c.6913C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354901.2:c.6859C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354902.2:c.6763C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354903.2:c.6733C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354904.2:c.6658C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354905.2:c.6556C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354906.2:c.6187C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
14

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000043137Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq
no assertion criteria provided
variant of unknown significance
(Jul 13, 2012)
germlineresearch

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

SCV000149027GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Sep 8, 2020)
germlineclinical testing

Citation Link,

SCV000600143Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics criteria)
Benign
(Jan 11, 2023)
unknownclinical testing

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

SCV000609172CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Likely benign
(Jul 1, 2024)
germlineclinical testing

Citation Link,

SCV002010860Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Nov 3, 2021)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes14not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineno1not providednot provided572not providedresearch
not providedgermlinenot providednot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Outcomes of retesting BRCA negative patients using multigene panels.

Yadav S, Reeves A, Campian S, Paine A, Zakalik D.

Fam Cancer. 2017 Jul;16(3):319-328. doi: 10.1007/s10689-016-9956-7.

PubMed [citation]
PMID:
27878467

Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.

Mandelker D, Zhang L, Kemel Y, Stadler ZK, Joseph V, Zehir A, Pradhan N, Arnold A, Walsh MF, Li Y, Balakrishnan AR, Syed A, Prasad M, Nafa K, Carlo MI, Cadoo KA, Sheehan M, Fleischut MH, Salo-Mullen E, Trottier M, Lipkin SM, Lincoln A, et al.

JAMA. 2017 Sep 5;318(9):825-835. doi: 10.1001/jama.2017.11137. Erratum in: JAMA. 2018 Dec 11;320(22):2381. doi: 10.1001/jama.2018.17511.

PubMed [citation]
PMID:
28873162
PMCID:
PMC5611881
See all PubMed Citations (7)

Details of each submission

From Biesecker Lab/Clinical Genomics Section, National Institutes of Health - ClinSeq, SCV000043137.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See PubMed ID:22703879 for details.

Description

Converted during submission to Uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineno572not provideddiscovery1not providednot providednot provided

From GeneDx, SCV000149027.15

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is associated with the following publications: (PMID: 24728327, 28873162, 22703879, 25203624, 27878467)

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000600143.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Center for Human Genetics Tuebingen, SCV000609172.31

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided14not providednot providedclinical testingnot provided

Description

APC: BS1

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided14not providednot providednot provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002010860.3

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

Last Updated: Oct 20, 2024