NM_000038.6(APC):c.4647del (p.Glu1550fs) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 9, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_000038.6(APC):c.4647del (p.Glu1550fs)]

NM_000038.6(APC):c.4647del (p.Glu1550fs)

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
Cytogenetic location:
Genomic location:
Preferred name:
NM_000038.6(APC):c.4647del (p.Glu1550fs)
  • NC_000005.10:g.112840241del
  • NG_008481.4:g.152721del
  • NM_000038.6:c.4647delMANE SELECT
  • NM_001127510.3:c.4647del
  • NM_001127511.3:c.4593del
  • NM_001354895.2:c.4647del
  • NM_001354896.2:c.4701del
  • NM_001354897.2:c.4677del
  • NM_001354898.2:c.4572del
  • NM_001354899.2:c.4563del
  • NM_001354900.2:c.4524del
  • NM_001354901.2:c.4470del
  • NM_001354902.2:c.4374del
  • NM_001354903.2:c.4344del
  • NM_001354904.2:c.4269del
  • NM_001354905.2:c.4167del
  • NM_001354906.2:c.3798del
  • NP_000029.2:p.Glu1550fs
  • NP_001120982.1:p.Glu1550fs
  • NP_001120983.2:p.Glu1532fs
  • NP_001341824.1:p.Glu1550fs
  • NP_001341825.1:p.Glu1568fs
  • NP_001341826.1:p.Glu1560fs
  • NP_001341827.1:p.Glu1525fs
  • NP_001341828.1:p.Glu1522fs
  • NP_001341829.1:p.Glu1509fs
  • NP_001341830.1:p.Glu1491fs
  • NP_001341831.1:p.Glu1459fs
  • NP_001341832.1:p.Glu1449fs
  • NP_001341833.1:p.Glu1424fs
  • NP_001341834.1:p.Glu1390fs
  • NP_001341835.1:p.Glu1267fs
  • LRG_130:g.152721del
  • NC_000005.9:g.112175938del
  • NM_000038.5:c.4647delA
  • p.Glu1550Argfs*15
Protein change:
dbSNP: rs879254283
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_000038.6:c.4647del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127510.3:c.4647del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127511.3:c.4593del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354895.2:c.4647del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354896.2:c.4701del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354897.2:c.4677del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354898.2:c.4572del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354899.2:c.4563del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354900.2:c.4524del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354901.2:c.4470del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354902.2:c.4374del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354903.2:c.4344del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354904.2:c.4269del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354905.2:c.4167del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354906.2:c.3798del - frameshift variant - [Sequence Ontology: SO:0001589]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000294051GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 9, 2016)
germlineclinical testing

Citation Link,

SCV000691752Mayo Clinic Laboratories, Mayo Clinicno assertion criteria providedLikely pathogenicunknownclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000294051.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


This deletion of one nucleotide in APC is denoted c.4647delA at the cDNA level and p.Glu1550ArgfsX15 (E1550RfsX15) at the protein level. The normal sequence, with the base that is deleted in braces, is ACCA[A]GAGA. The deletion causes a frameshift which changes a Glutamic Acid to an Arginine at codon 1550, and creates a premature stop codon at position 15 of the new reading frame. Even though this frameshift occurs in the last exon of the gene, and nonsense-mediated decay is not expected to occur, it is significant since the last 1294 amino acids are replaced with 14 incorrect amino acids. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through protein truncation. We consider this variant to be likely pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV000691752.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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