NM_000038.6(APC):c.7802G>A (p.Ser2601Asn) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 14, 2022
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:: RCV000584158.17

Allele description [Variation Report for NM_000038.6(APC):c.7802G>A (p.Ser2601Asn)]

NM_000038.6(APC):c.7802G>A (p.Ser2601Asn)

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.7802G>A (p.Ser2601Asn)

HGVS:

NC_000005.10:g.112843396G>A
NG_008481.4:g.155876G>A
NM_000038.6:c.7802G>AMANE SELECT
NM_001127510.3:c.7802G>A
NM_001127511.3:c.7748G>A
NM_001354895.2:c.7802G>A
NM_001354896.2:c.7856G>A
NM_001354897.2:c.7832G>A
NM_001354898.2:c.7727G>A
NM_001354899.2:c.7718G>A
NM_001354900.2:c.7679G>A
NM_001354901.2:c.7625G>A
NM_001354902.2:c.7529G>A
NM_001354903.2:c.7499G>A
NM_001354904.2:c.7424G>A
NM_001354905.2:c.7322G>A
NM_001354906.2:c.6953G>A
NP_000029.2:p.Ser2601Asn
NP_001120982.1:p.Ser2601Asn
NP_001120983.2:p.Ser2583Asn
NP_001341824.1:p.Ser2601Asn
NP_001341825.1:p.Ser2619Asn
NP_001341826.1:p.Ser2611Asn
NP_001341827.1:p.Ser2576Asn
NP_001341828.1:p.Ser2573Asn
NP_001341829.1:p.Ser2560Asn
NP_001341830.1:p.Ser2542Asn
NP_001341831.1:p.Ser2510Asn
NP_001341832.1:p.Ser2500Asn
NP_001341833.1:p.Ser2475Asn
NP_001341834.1:p.Ser2441Asn
NP_001341835.1:p.Ser2318Asn
LRG_130:g.155876G>A
NC_000005.9:g.112179093G>A
NM_000038.5:c.7802G>A

Protein change:

S2318N

Links:

dbSNP: rs1554088668

NCBI 1000 Genomes Browser:

rs1554088668

Molecular consequence:

NM_000038.6:c.7802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7748G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7802G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7856G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7832G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7727G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7718G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7679G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7625G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7529G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7499G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7424G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7322G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6953G>A - 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
SCV000687143	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 14, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001189287	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 11, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000687143

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 14, 2022)

germline

clinical testing

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

SCV001189287

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 11, 2022)

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	unknown	not provided	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

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000687143.5

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

Description

This missense variant replaces serine with asparagine at codon 2601 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with APC-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	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, SCV001189287.4

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

Description

The p.S2601N variant (also known as c.7802G>A), located in coding exon 15 of the APC gene, results from a G to A substitution at nucleotide position 7802. The serine at codon 2601 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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 3, 2024

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