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NM_000038.6(APC):c.937_938del (p.Glu313fs) AND Familial adenomatous polyposis 1

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 1, 1999
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:
RCV000000874.17

Allele description [Variation Report for NM_000038.6(APC):c.937_938del (p.Glu313fs)]

NM_000038.6(APC):c.937_938del (p.Glu313fs)

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.937_938del (p.Glu313fs)
HGVS:
  • NC_000005.10:g.112818969_112818970del
  • NG_008481.4:g.131449_131450del
  • NM_000038.6:c.937_938delMANE SELECT
  • NM_001127510.3:c.937_938del
  • NM_001127511.3:c.883_884del
  • NM_001354895.2:c.937_938del
  • NM_001354896.2:c.937_938del
  • NM_001354897.2:c.967_968del
  • NM_001354898.2:c.862_863del
  • NM_001354899.2:c.853_854del
  • NM_001354900.2:c.760_761del
  • NM_001354901.2:c.760_761del
  • NM_001354902.2:c.964-300_964-299del
  • NM_001354903.2:c.934-300_934-299del
  • NM_001354904.2:c.859-300_859-299del
  • NM_001354905.2:c.757-300_757-299del
  • NM_001354906.2:c.88_89del
  • NP_000029.2:p.Glu313fs
  • NP_001120982.1:p.Glu313fs
  • NP_001120983.2:p.Glu295fs
  • NP_001341824.1:p.Glu313fs
  • NP_001341825.1:p.Glu313fs
  • NP_001341826.1:p.Glu323fs
  • NP_001341827.1:p.Glu288fs
  • NP_001341828.1:p.Glu285fs
  • NP_001341829.1:p.Glu254fs
  • NP_001341830.1:p.Glu254fs
  • NP_001341835.1:p.Glu30fs
  • LRG_130:g.131449_131450del
  • NC_000005.9:g.112154666_112154667del
  • NM_000038.5:c.937_938del
  • NM_000038.5:c.937_938delGA
Protein change:
E254fs
Links:
OMIM: 611731.0038; dbSNP: rs387906239
NCBI 1000 Genomes Browser:
rs387906239
Molecular consequence:
  • NM_000038.6:c.937_938del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127510.3:c.937_938del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127511.3:c.883_884del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354895.2:c.937_938del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354896.2:c.937_938del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354897.2:c.967_968del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354898.2:c.862_863del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354899.2:c.853_854del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354900.2:c.760_761del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354901.2:c.760_761del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354906.2:c.88_89del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354902.2:c.964-300_964-299del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354903.2:c.934-300_934-299del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354904.2:c.859-300_859-299del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001354905.2:c.757-300_757-299del - intron variant - [Sequence Ontology: SO:0001627]
Observations:
7

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000021024OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 1999) 		germlineliterature only

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

SCV000591060Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Pathogenicunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyes7not providednot providednot providednot providedclinical testing

Citations

PubMed

Familial adenomatous polyposis-associated thyroid cancer: a clinical, pathological, and molecular genetics study.

Soravia C, Sugg SL, Berk T, Mitri A, Cheng H, Gallinger S, Cohen Z, Asa SL, Bapat BV.

Am J Pathol. 1999 Jan;154(1):127-35.

PubMed [citation]
PMID:
9916927
PMCID:
PMC1853451

Details of each submission

From OMIM, SCV000021024.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a family with an attenuated form of adenomatous polyposis coli (see 175100) and thyroid cancer, Soravia et al. (1999) identified a germline 2-bp deletion (937delGA) in exon 9 of the APC gene, resulting in a frameshift and a premature stop codon. The thyroid tumors showed a range of morphologic features: some exhibited typical papillary architecture and were associated with multifocal carcinoma; in others, there were unusual areas of cribriform morphology, and spindle-cell components with whorled architecture. RET/PTC1 and RET/PTC3 (see 164761) were expressed in thyroid cancers.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591060.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided7not providednot providedclinical testingnot provided

Description

The APC p.Glu313AsnfsX13 variant was not identified in the literature, nor was it identified in, the 1000 Genomes Project, the NHLBI Exome Sequencing Project, the Exome Aggregation Consortium, the Genome Aggregation Database (Feb 27, 2017), Clinvitae, UMD, InSiGHT Colon Cancer Gene Variant Database (LOVD), or the Zhejiang Colon Cancer Database (LOVD). The variant was identified in dbSNP (ID: rs387906239) as “With Pathogenic allele”, GeneInsight COGR (classified as pathogenic) and ClinVar (classified as pathogenic by GeneDx and OMIM) databases. The c.937_938delGA variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 313 and leads to a premature stop codon 13 codons downstream. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the APC gene are an established mechanism of disease in familial adenomatous polyposis and is the type of variant expected to cause the disorder. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided7not providednot providednot provided

Last Updated: Apr 20, 2024