NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 22, 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:: RCV003537120.1

Allele description

NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del)

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.7130_7144del (p.Asn2377_Gln2381del)

HGVS:

NC_000005.10:g.112842724_112842738del
NG_008481.4:g.155204_155218del
NM_000038.6:c.7130_7144delMANE SELECT
NM_001127510.3:c.7130_7144del
NM_001127511.3:c.7076_7090del
NM_001354895.2:c.7130_7144del
NM_001354896.2:c.7184_7198del
NM_001354897.2:c.7160_7174del
NM_001354898.2:c.7055_7069del
NM_001354899.2:c.7046_7060del
NM_001354900.2:c.7007_7021del
NM_001354901.2:c.6953_6967del
NM_001354902.2:c.6857_6871del
NM_001354903.2:c.6827_6841del
NM_001354904.2:c.6752_6766del
NM_001354905.2:c.6650_6664del
NM_001354906.2:c.6281_6295del
NP_000029.2:p.Asn2377_Gln2381del
NP_001120982.1:p.Asn2377_Gln2381del
NP_001120983.2:p.Asn2359_Gln2363del
NP_001341824.1:p.Asn2377_Gln2381del
NP_001341825.1:p.Asn2395_Gln2399del
NP_001341826.1:p.Asn2387_Gln2391del
NP_001341827.1:p.Asn2352_Gln2356del
NP_001341828.1:p.Asn2349_Gln2353del
NP_001341829.1:p.Asn2336_Gln2340del
NP_001341830.1:p.Asn2318_Gln2322del
NP_001341831.1:p.Asn2286_Gln2290del
NP_001341832.1:p.Asn2276_Gln2280del
NP_001341833.1:p.Asn2251_Gln2255del
NP_001341834.1:p.Asn2217_Gln2221del
NP_001341835.1:p.Asn2094_Gln2098del
LRG_130t1:c.7130_7144del
LRG_130:g.155204_155218del
NC_000005.9:g.112178420_112178434del
NC_000005.9:g.112178421_112178435del
NM_000038.4:c.7130_7144delACCTTACCAAACAAA
NM_000038.5:c.7130_7144del15

Links:

dbSNP: rs1472879431

NCBI 1000 Genomes Browser:

rs1472879431

Molecular consequence:

NM_000038.6:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127510.3:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127511.3:c.7076_7090del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354895.2:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354896.2:c.7184_7198del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354897.2:c.7160_7174del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354898.2:c.7055_7069del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354899.2:c.7046_7060del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354900.2:c.7007_7021del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354901.2:c.6953_6967del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354902.2:c.6857_6871del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354903.2:c.6827_6841del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354904.2:c.6752_6766del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354905.2:c.6650_6664del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354906.2:c.6281_6295del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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Mus musculus ceramide synthase 5 (Cers5), mRNA
Mus musculus ceramide synthase 5 (Cers5), mRNA
gi|31980682|ref|NM_028015.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002269139	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 22, 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

SCV002269139

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 22, 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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002269139.3

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

Description

This variant, c.7130_7144del, results in the deletion of 5 amino acid(s) of the APC protein (p.Asn2377_Gln2381del), but otherwise preserves the integrity of the reading frame. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 482291). This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%).

#	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: Jun 2, 2024

ClinVar

Relating variation to medicine