NM_000038.6(APC):c.7502C>A (p.Ala2501Asp) AND Classic or attenuated familial adenomatous polyposis

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 30, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV004015876.2

Allele description [Variation Report for NM_000038.6(APC):c.7502C>A (p.Ala2501Asp)]

NM_000038.6(APC):c.7502C>A (p.Ala2501Asp)

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.7502C>A (p.Ala2501Asp)

HGVS:

NC_000005.10:g.112843096C>A
NG_008481.4:g.155576C>A
NM_000038.6:c.7502C>AMANE SELECT
NM_001127510.3:c.7502C>A
NM_001127511.3:c.7448C>A
NM_001354895.2:c.7502C>A
NM_001354896.2:c.7556C>A
NM_001354897.2:c.7532C>A
NM_001354898.2:c.7427C>A
NM_001354899.2:c.7418C>A
NM_001354900.2:c.7379C>A
NM_001354901.2:c.7325C>A
NM_001354902.2:c.7229C>A
NM_001354903.2:c.7199C>A
NM_001354904.2:c.7124C>A
NM_001354905.2:c.7022C>A
NM_001354906.2:c.6653C>A
NM_001407446.1:c.7586C>A
NM_001407447.1:c.7556C>A
NM_001407448.1:c.7556C>A
NM_001407449.1:c.7556C>A
NM_001407450.1:c.7502C>A
NM_001407451.1:c.7481C>A
NM_001407452.1:c.7472C>A
NM_001407453.1:c.7325C>A
NM_001407454.1:c.7253C>A
NM_001407455.1:c.7253C>A
NM_001407456.1:c.7253C>A
NM_001407457.1:c.7253C>A
NM_001407458.1:c.7199C>A
NM_001407459.1:c.7199C>A
NM_001407460.1:c.7199C>A
NM_001407467.1:c.7115C>A
NM_001407469.1:c.7115C>A
NM_001407470.1:c.6653C>A
NM_001407471.1:c.6350C>A
NM_001407472.1:c.6350C>A
NP_000029.2:p.Ala2501Asp
NP_000029.2:p.Ala2501Asp
NP_001120982.1:p.Ala2501Asp
NP_001120982.1:p.Ala2501Asp
NP_001120983.1:p.Ala2501Asp
NP_001120983.2:p.Ala2483Asp
NP_001341824.1:p.Ala2501Asp
NP_001341825.1:p.Ala2519Asp
NP_001341826.1:p.Ala2511Asp
NP_001341827.1:p.Ala2476Asp
NP_001341828.1:p.Ala2473Asp
NP_001341829.1:p.Ala2460Asp
NP_001341830.1:p.Ala2442Asp
NP_001341831.1:p.Ala2410Asp
NP_001341832.1:p.Ala2400Asp
NP_001341833.1:p.Ala2375Asp
NP_001341834.1:p.Ala2341Asp
NP_001341835.1:p.Ala2218Asp
NP_001394375.1:p.Ala2529Asp
NP_001394376.1:p.Ala2519Asp
NP_001394377.1:p.Ala2519Asp
NP_001394378.1:p.Ala2519Asp
NP_001394379.1:p.Ala2501Asp
NP_001394380.1:p.Ala2494Asp
NP_001394381.1:p.Ala2491Asp
NP_001394382.1:p.Ala2442Asp
NP_001394383.1:p.Ala2418Asp
NP_001394384.1:p.Ala2418Asp
NP_001394385.1:p.Ala2418Asp
NP_001394386.1:p.Ala2418Asp
NP_001394387.1:p.Ala2400Asp
NP_001394388.1:p.Ala2400Asp
NP_001394389.1:p.Ala2400Asp
NP_001394396.1:p.Ala2372Asp
NP_001394398.1:p.Ala2372Asp
NP_001394399.1:p.Ala2218Asp
NP_001394400.1:p.Ala2117Asp
NP_001394401.1:p.Ala2117Asp
LRG_130t1:c.7502C>A
LRG_130t2:c.7502C>A
LRG_130t3:c.7502C>A
LRG_130:g.155576C>A
LRG_130p1:p.Ala2501Asp
LRG_130p2:p.Ala2501Asp
LRG_130p3:p.Ala2501Asp
NC_000005.9:g.112178793C>A
NM_000038.4:c.7502C>A
NM_001127510.1:c.7502C>A
NM_001127511.1:c.7502C>A
NR_176365.1:n.7337C>A
NR_176366.1:n.7756C>A

Protein change:

A2117D

Molecular consequence:

NM_000038.6:c.7502C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7502C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7448C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7502C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7556C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7532C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7427C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7418C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7379C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7325C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7229C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7199C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7124C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7022C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6653C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7586C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7556C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7556C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7556C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7502C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7481C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7472C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7325C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7253C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7253C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7253C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7253C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7199C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7199C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7199C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7115C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7115C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6653C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6350C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6350C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176365.1:n.7337C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.7756C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Classic or attenuated familial adenomatous polyposis
Identifiers:: MONDO: MONDO:0021057; MedGen: CN372698

Recent activity

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Mus musculus immunoglobulin superfamily containing leucine-rich repeat 2 (Islr2)...
Mus musculus immunoglobulin superfamily containing leucine-rich repeat 2 (Islr2), transcript variant 8, mRNA
gi|238859615|ref|NM_001161541.1|

Nucleotide
719239[uid] AND (alive[prop]) (1)
Gene
FLT3LG fms related receptor tyrosine kinase 3 ligand [Macaca mulatta]
FLT3LG fms related receptor tyrosine kinase 3 ligand [Macaca mulatta]
Gene ID:719239

Gene
Hif1an hypoxia-inducible factor 1, alpha subunit inhibitor [Mus musculus]
Hif1an hypoxia-inducible factor 1, alpha subunit inhibitor [Mus musculus]
Gene ID:319594

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004826174	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (May 30, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004826174

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(May 30, 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	1	not provided	not provided	108544	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 All of Us Research Program, National Institutes of Health, SCV004826174.1

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

Description

This missense variant replaces alanine with aspartic acid at codon 2501 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	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: May 7, 2024

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