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NM_000038.6(APC):c.7849_7853del (p.Lys2616_Glu2617insTer) AND Classic or attenuated familial adenomatous polyposis

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 8, 2024
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:
RCV004009751.2

Allele description [Variation Report for NM_000038.6(APC):c.7849_7853del (p.Lys2616_Glu2617insTer)]

NM_000038.6(APC):c.7849_7853del (p.Lys2616_Glu2617insTer)

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.7849_7853del (p.Lys2616_Glu2617insTer)
HGVS:
  • NC_000005.10:g.112843443_112843447del
  • NG_008481.4:g.155923_155927del
  • NM_000038.6:c.7849_7853delMANE SELECT
  • NM_001127510.3:c.7849_7853del
  • NM_001127511.3:c.7795_7799del
  • NM_001354895.2:c.7849_7853del
  • NM_001354896.2:c.7903_7907del
  • NM_001354897.2:c.7879_7883del
  • NM_001354898.2:c.7774_7778del
  • NM_001354899.2:c.7765_7769del
  • NM_001354900.2:c.7726_7730del
  • NM_001354901.2:c.7672_7676del
  • NM_001354902.2:c.7576_7580del
  • NM_001354903.2:c.7546_7550del
  • NM_001354904.2:c.7471_7475del
  • NM_001354905.2:c.7369_7373del
  • NM_001354906.2:c.7000_7004del
  • NM_001407446.1:c.7933_7937del
  • NM_001407447.1:c.7903_7907del
  • NM_001407448.1:c.7903_7907del
  • NM_001407449.1:c.7903_7907del
  • NM_001407450.1:c.7849_7853del
  • NM_001407451.1:c.7828_7832del
  • NM_001407452.1:c.7819_7823del
  • NM_001407453.1:c.7672_7676del
  • NM_001407454.1:c.7600_7604del
  • NM_001407455.1:c.7600_7604del
  • NM_001407456.1:c.7600_7604del
  • NM_001407457.1:c.7600_7604del
  • NM_001407458.1:c.7546_7550del
  • NM_001407459.1:c.7546_7550del
  • NM_001407460.1:c.7546_7550del
  • NM_001407467.1:c.7462_7466del
  • NM_001407469.1:c.7462_7466del
  • NM_001407470.1:c.7000_7004del
  • NM_001407471.1:c.6697_6701del
  • NM_001407472.1:c.6697_6701del
  • NP_000029.2:p.Glu2617Terfs
  • NP_000029.2:p.Lys2616_Glu2617insTer
  • NP_001120982.1:p.Glu2617Terfs
  • NP_001120982.1:p.Lys2616_Glu2617insTer
  • NP_001120983.1:p.Glu2617Terfs
  • NP_001120983.2:p.Lys2598_Glu2599insTer
  • NP_001341824.1:p.Lys2616_Glu2617insTer
  • NP_001341825.1:p.Lys2634_Glu2635insTer
  • NP_001341826.1:p.Lys2626_Glu2627insTer
  • NP_001341827.1:p.Lys2591_Glu2592insTer
  • NP_001341828.1:p.Lys2588_Glu2589insTer
  • NP_001341829.1:p.Lys2575_Glu2576insTer
  • NP_001341830.1:p.Lys2557_Glu2558insTer
  • NP_001341831.1:p.Lys2525_Glu2526insTer
  • NP_001341832.1:p.Lys2515_Glu2516insTer
  • NP_001341833.1:p.Lys2490_Glu2491insTer
  • NP_001341834.1:p.Lys2456_Glu2457insTer
  • NP_001341835.1:p.Lys2333_Glu2334insTer
  • NP_001394375.1:p.Lys2644_Glu2645insTer
  • NP_001394376.1:p.Lys2634_Glu2635insTer
  • NP_001394377.1:p.Lys2634_Glu2635insTer
  • NP_001394378.1:p.Lys2634_Glu2635insTer
  • NP_001394379.1:p.Lys2616_Glu2617insTer
  • NP_001394380.1:p.Lys2609_Glu2610insTer
  • NP_001394381.1:p.Lys2606_Glu2607insTer
  • NP_001394382.1:p.Lys2557_Glu2558insTer
  • NP_001394383.1:p.Lys2533_Glu2534insTer
  • NP_001394384.1:p.Lys2533_Glu2534insTer
  • NP_001394385.1:p.Lys2533_Glu2534insTer
  • NP_001394386.1:p.Lys2533_Glu2534insTer
  • NP_001394387.1:p.Lys2515_Glu2516insTer
  • NP_001394388.1:p.Lys2515_Glu2516insTer
  • NP_001394389.1:p.Lys2515_Glu2516insTer
  • NP_001394396.1:p.Lys2487_Glu2488insTer
  • NP_001394398.1:p.Lys2487_Glu2488insTer
  • NP_001394399.1:p.Lys2333_Glu2334insTer
  • NP_001394400.1:p.Lys2232_Glu2233insTer
  • NP_001394401.1:p.Lys2232_Glu2233insTer
  • LRG_130t1:c.7849_7853del
  • LRG_130t2:c.7849_7853del
  • LRG_130t3:c.7849_7853del
  • LRG_130:g.155923_155927del
  • LRG_130p1:p.Glu2617Terfs
  • LRG_130p2:p.Glu2617Terfs
  • LRG_130p3:p.Glu2617Terfs
  • NC_000005.9:g.112179140_112179144del
  • NM_000038.4:c.7849_7853delGAAAA
  • NM_001127510.1:c.7849_7853delGAAAA
  • NM_001127511.1:c.7849_7853delGAAAA
  • NR_176365.1:n.7684_7688del
  • NR_176366.1:n.8103_8107del
Molecular consequence:
  • NR_176365.1:n.7684_7688del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176366.1:n.8103_8107del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000038.6:c.7849_7853del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001127510.3:c.7849_7853del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001127511.3:c.7795_7799del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354895.2:c.7849_7853del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354896.2:c.7903_7907del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354897.2:c.7879_7883del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354898.2:c.7774_7778del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354899.2:c.7765_7769del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354900.2:c.7726_7730del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354901.2:c.7672_7676del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354902.2:c.7576_7580del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354903.2:c.7546_7550del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354904.2:c.7471_7475del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354905.2:c.7369_7373del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354906.2:c.7000_7004del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407446.1:c.7933_7937del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407447.1:c.7903_7907del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407448.1:c.7903_7907del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407449.1:c.7903_7907del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407450.1:c.7849_7853del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407451.1:c.7828_7832del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407452.1:c.7819_7823del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407453.1:c.7672_7676del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407454.1:c.7600_7604del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407455.1:c.7600_7604del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407456.1:c.7600_7604del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407457.1:c.7600_7604del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407458.1:c.7546_7550del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407459.1:c.7546_7550del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407460.1:c.7546_7550del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407467.1:c.7462_7466del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407469.1:c.7462_7466del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407470.1:c.7000_7004del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407471.1:c.6697_6701del - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001407472.1:c.6697_6701del - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004839128All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jan 8, 2024) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided108544not providedclinical testing

Citations

PubMed

The ABC of APC.

Fearnhead NS, Britton MP, Bodmer WF.

Hum Mol Genet. 2001 Apr;10(7):721-33. Review.

PubMed [citation]
PMID:
11257105

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, SCV004839128.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (2)

Description

This variant deletes 5 nucleotides in exon 16 of the APC gene, creating a frameshift and premature translation stop signal in the last coding exon. This variant is predicted to escape nonsense-mediated decay and be expressed as a truncated protein. Although functional studies have not been reported, this variant is expected to disrupt the EB1 and HDLG binding domains (PMID: 11257105). To our knowledge, 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). Loss of APC function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Oct 13, 2024