NM_000038.6(APC):c.3049_3051del (p.Asn1017del) AND Classic or attenuated familial adenomatous polyposis

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 23, 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:: RCV003998397.2

Allele description [Variation Report for NM_000038.6(APC):c.3049_3051del (p.Asn1017del)]

NM_000038.6(APC):c.3049_3051del (p.Asn1017del)

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.3049_3051del (p.Asn1017del)

HGVS:

NC_000005.10:g.112838643_112838645del
NG_008481.4:g.151123_151125del
NM_000038.6:c.3049_3051delMANE SELECT
NM_001127510.3:c.3049_3051del
NM_001127511.3:c.2995_2997del
NM_001354895.2:c.3049_3051del
NM_001354896.2:c.3103_3105del
NM_001354897.2:c.3079_3081del
NM_001354898.2:c.2974_2976del
NM_001354899.2:c.2965_2967del
NM_001354900.2:c.2926_2928del
NM_001354901.2:c.2872_2874del
NM_001354902.2:c.2776_2778del
NM_001354903.2:c.2746_2748del
NM_001354904.2:c.2671_2673del
NM_001354905.2:c.2569_2571del
NM_001354906.2:c.2200_2202del
NP_000029.2:p.Asn1017del
NP_001120982.1:p.Asn1017del
NP_001120983.2:p.Asn999del
NP_001341824.1:p.Asn1017del
NP_001341825.1:p.Asn1035del
NP_001341826.1:p.Asn1027del
NP_001341827.1:p.Asn992del
NP_001341828.1:p.Asn989del
NP_001341829.1:p.Asn976del
NP_001341830.1:p.Asn958del
NP_001341831.1:p.Asn926del
NP_001341832.1:p.Asn916del
NP_001341833.1:p.Asn891del
NP_001341834.1:p.Asn857del
NP_001341835.1:p.Asn734del
LRG_130:g.151123_151125del
NC_000005.9:g.112174338_112174340del
NC_000005.9:g.112174340_112174342del
NM_000038.5:c.3049_3051delAAT
p.N1017del

Protein change:

N1017del

Links:

dbSNP: rs730881229

NCBI 1000 Genomes Browser:

rs730881229

Molecular consequence:

NM_000038.6:c.3049_3051del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127510.3:c.3049_3051del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127511.3:c.2995_2997del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354895.2:c.3049_3051del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354896.2:c.3103_3105del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354897.2:c.3079_3081del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354898.2:c.2974_2976del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354899.2:c.2965_2967del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354900.2:c.2926_2928del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354901.2:c.2872_2874del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354902.2:c.2776_2778del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354903.2:c.2746_2748del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354904.2:c.2671_2673del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354905.2:c.2569_2571del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354906.2:c.2200_2202del - inframe_deletion - [Sequence Ontology: SO:0001822]

Observations:

Condition(s)

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

Recent activity

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secreted frizzled-related protein 1a isoform X1 [Eleginops maclovinus]
secreted frizzled-related protein 1a isoform X1 [Eleginops maclovinus]
gi|2702190286|ref|XP_063752518.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004839763	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Aug 23, 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

SCV004839763

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Aug 23, 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	2	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, SCV004839763.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

Description

This variant causes an in-frame deletion of 1 amino acids at exon 16 of the APC protein. 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 been identified in 1/251128 chromosomes 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		2	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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