NM_000038.6(APC):c.1892_1904delinsAAT (p.Ile631fs) AND Familial adenomatous polyposis 1

Clinical significance:Pathogenic (Last evaluated: Jun 25, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000227617.2

Allele description [Variation Report for NM_000038.6(APC):c.1892_1904delinsAAT (p.Ile631fs)]

NM_000038.6(APC):c.1892_1904delinsAAT (p.Ile631fs)

Gene:
APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
5q22.2
Genomic location:
Preferred name:
NM_000038.6(APC):c.1892_1904delinsAAT (p.Ile631fs)
HGVS:
  • NC_000005.10:g.112835099_112835111delinsAAT
  • NG_008481.4:g.147579_147591delinsAAT
  • NM_000038.6:c.1892_1904delinsAATMANE SELECT
  • NM_001127510.3:c.1892_1904delinsAAT
  • NM_001127511.3:c.1838_1850delinsAAT
  • NM_001354895.2:c.1892_1904delinsAAT
  • NM_001354896.2:c.1946_1958delinsAAT
  • NM_001354897.2:c.1922_1934delinsAAT
  • NM_001354898.2:c.1817_1829delinsAAT
  • NM_001354899.2:c.1808_1820delinsAAT
  • NM_001354900.2:c.1769_1781delinsAAT
  • NM_001354901.2:c.1715_1727delinsAAT
  • NM_001354902.2:c.1619_1631delinsAAT
  • NM_001354903.2:c.1589_1601delinsAAT
  • NM_001354904.2:c.1514_1526delinsAAT
  • NM_001354905.2:c.1412_1424delinsAAT
  • NM_001354906.2:c.1043_1055delinsAAT
  • NP_000029.2:p.Ile631fs
  • NP_001120982.1:p.Ile631fs
  • NP_001120983.2:p.Ile613fs
  • NP_001341824.1:p.Ile631fs
  • NP_001341825.1:p.Ile649fs
  • NP_001341826.1:p.Ile641fs
  • NP_001341827.1:p.Ile606fs
  • NP_001341828.1:p.Ile603fs
  • NP_001341829.1:p.Ile590fs
  • NP_001341830.1:p.Ile572fs
  • NP_001341831.1:p.Ile540fs
  • NP_001341832.1:p.Ile530fs
  • NP_001341833.1:p.Ile505fs
  • NP_001341834.1:p.Ile471fs
  • NP_001341835.1:p.Ile348fs
  • LRG_130:g.147579_147591delinsAAT
  • NC_000005.9:g.112170796_112170808delinsAAT
  • NM_000038.5:c.1892_1904delTTATTGAAAGTGGinsAAT
  • NM_000038.5:c.1892_1904delinsAAT
Protein change:
I348fs
Links:
dbSNP: rs863225319
NCBI 1000 Genomes Browser:
rs863225319
Molecular consequence:
  • NM_000038.6:c.1892_1904delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127510.3:c.1892_1904delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127511.3:c.1838_1850delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354895.2:c.1892_1904delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354896.2:c.1946_1958delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354897.2:c.1922_1934delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354898.2:c.1817_1829delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354899.2:c.1808_1820delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354900.2:c.1769_1781delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354901.2:c.1715_1727delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354902.2:c.1619_1631delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354903.2:c.1589_1601delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354904.2:c.1514_1526delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354905.2:c.1412_1424delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354906.2:c.1043_1055delinsAAT - frameshift variant - [Sequence Ontology: SO:0001589]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000282706Invitaecriteria provided, single submitter
Pathogenic
(Jun 25, 2016)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000282706.3

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

Description

This sequence change deletes 13 nucleotides and inserts 3 nucleotides in exon 15 of the APC mRNA (c.1892_1904delTTATTGAAAGTGGinsAAT), causing a frameshift at codon 631. This creates a premature translational stop signal (p.Ile631Lysfs*2) and is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, truncating variants in APC are known to be pathogenic (PMID: 20685668, 17963004). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 7, 2021

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