NM_000038.6(APC):c.3949G>C (p.Glu1317Gln) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Jun 2, 2023
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:: RCV000579405.16

Allele description [Variation Report for NM_000038.6(APC):c.3949G>C (p.Glu1317Gln)]

NM_000038.6(APC):c.3949G>C (p.Glu1317Gln)

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.3949G>C (p.Glu1317Gln)

Other names:

p.E1317Q:GAA>CAA; CCDS4107.1:c.3949G>C

HGVS:

NC_000005.10:g.112839543G>C
NG_008481.4:g.152023G>C
NM_000038.6:c.3949G>CMANE SELECT
NM_001127510.3:c.3949G>C
NM_001127511.3:c.3895G>C
NM_001354895.2:c.3949G>C
NM_001354896.2:c.4003G>C
NM_001354897.2:c.3979G>C
NM_001354898.2:c.3874G>C
NM_001354899.2:c.3865G>C
NM_001354900.2:c.3826G>C
NM_001354901.2:c.3772G>C
NM_001354902.2:c.3676G>C
NM_001354903.2:c.3646G>C
NM_001354904.2:c.3571G>C
NM_001354905.2:c.3469G>C
NM_001354906.2:c.3100G>C
NP_000029.2:p.Glu1317Gln
NP_001120982.1:p.Glu1317Gln
NP_001120983.2:p.Glu1299Gln
NP_001341824.1:p.Glu1317Gln
NP_001341825.1:p.Glu1335Gln
NP_001341826.1:p.Glu1327Gln
NP_001341827.1:p.Glu1292Gln
NP_001341828.1:p.Glu1289Gln
NP_001341829.1:p.Glu1276Gln
NP_001341830.1:p.Glu1258Gln
NP_001341831.1:p.Glu1226Gln
NP_001341832.1:p.Glu1216Gln
NP_001341833.1:p.Glu1191Gln
NP_001341834.1:p.Glu1157Gln
NP_001341835.1:p.Glu1034Gln
LRG_130t1:c.3949G>C
LRG_130:g.152023G>C
NC_000005.9:g.112175240G>C
NM_000038.3:c.3949G>C
NM_000038.4:c.3949G>C
NM_000038.5:c.3949G>C
NM_001127510.2:c.3949G>C
NM_001127511.2:c.3895G>C
P25054:p.Glu1317Gln
c.3949G>C

Protein change:

E1034Q; GLU1317GLN

Links:

UniProtKB: P25054#VAR_009617; OMIM: 611731.0036; dbSNP: rs1801166

NCBI 1000 Genomes Browser:

rs1801166

Molecular consequence:

NM_000038.6:c.3949G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.3949G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.3895G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.3949G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.4003G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.3979G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.3874G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.3865G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.3826G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.3772G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.3676G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.3646G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.3571G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.3469G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.3100G>C - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000681643	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 30, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000693481	True Health Diagnostics	no assertion criteria provided	Likely benign (Aug 11, 2017)	germline	clinical testing
SCV001183123	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Dec 26, 2019)	germline	clinical testing	Citation Link,
SCV002536204	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Jul 28, 2020)	germline	curation	Citation Link,
SCV004015000	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jun 2, 2023)	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, curation

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

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000681643.2

#	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 True Health Diagnostics, SCV000693481.1

#	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 Ambry Genetics, SCV001183123.4

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

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.

#	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 Sema4, Sema4, SCV002536204.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	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 Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., SCV004015000.1

#	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: Nov 24, 2024

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