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NM_000038.6(APC):c.385G>C (p.Glu129Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(5);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Sep 29, 2021)
Last evaluated:
Dec 2, 2020
Accession:
VCV000133539.12
Variation ID:
133539
Description:
single nucleotide variant
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NM_000038.6(APC):c.385G>C (p.Glu129Gln)

Allele ID
137278
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q22.2
Genomic location
5: 112767353 (GRCh38) GRCh38 UCSC
5: 112103050 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_130:g.79833G>C
NC_000005.10:g.112767353G>C
NC_000005.9:g.112103050G>C
... more HGVS
Protein change
E129Q, E139Q, E70Q, E104Q
Other names
-
Canonical SPDI
NC_000005.10:112767352:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (C)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00005
Trans-Omics for Precision Medicine (TOPMed) 0.00002
1000 Genomes Project 0.00020
The Genome Aggregation Database (gnomAD), exomes 0.00008
Links
ClinGen: CA008713
dbSNP: rs376628500
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Apr 7, 2020 RCV000216893.6
Likely benign 5 criteria provided, multiple submitters, no conflicts Dec 13, 2019 RCV000589545.5
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 2, 2020 RCV000196705.9
not provided 1 no assertion provided Sep 19, 2013 RCV000120050.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
APC Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
9015 9049

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Dec 13, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001470644.1
Submitted: (Dec 31, 2020)
Evidence details
Publications
PubMed (2)
Likely benign
(May 09, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000694039.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: The APC c.385G>C (p.Glu129Gln) variant involves the alteration of a conserved nucleotide. 2/4 in silico tools predict a benign outcome (SNPs&GO not captured … (more)
Likely benign
(Nov 18, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000273092.5
Submitted: (Nov 30, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Co-occurence with a mutation in another gene that clearly explains a proband's phenotype;In silico models in agreement (benign);Other data supporting benign classification
Benign
(Dec 02, 2020)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: germline
Invitae
Accession: SCV000254011.9
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Likely benign
(May 29, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000490404.2
Submitted: (Sep 29, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 24728327, 28615371, 29753010, 30093976)
Uncertain significance
(Sep 26, 2016)
criteria provided, single submitter
Method: clinical testing
Familial adenomatous polyposis 1
Allele origin: unknown
Counsyl
Accession: SCV000489348.1
Submitted: (Nov 23, 2016)
Evidence details
Likely benign
(Apr 07, 2020)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000681635.3
Submitted: (May 19, 2020)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001922571.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001799446.1
Submitted: (Aug 19, 2021)
Evidence details
not provided
(Sep 19, 2013)
no assertion provided
Method: reference population
AllHighlyPenetrant
Allele origin: germline
ITMI
Accession: SCV000084186.1
Submitted: (May 29, 2014)
Comment:
Please see associated publication for description of ethnicities
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Secondary resistance to immunotherapy associated with β-catenin pathway activation or PTEN loss in metastatic melanoma. Trujillo JA Journal for immunotherapy of cancer 2019 PMID: 31703593
Clinical genetic testing outcome with multi-gene panel in Asian patients with multiple primary cancers. Chan GHJ Oncotarget 2018 PMID: 30093976
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. Bodian DL PloS one 2014 PMID: 24728327

Text-mined citations for rs376628500...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 06, 2021