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NM_004655.4(AXIN2):c.2038_2039del (p.Thr680fs) AND Oligodontia-cancer predisposition syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 8, 2022
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:
RCV001891838.4

Allele description [Variation Report for NM_004655.4(AXIN2):c.2038_2039del (p.Thr680fs)]

NM_004655.4(AXIN2):c.2038_2039del (p.Thr680fs)

Gene:
AXIN2:axin 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
17q24.1
Genomic location:
Preferred name:
NM_004655.4(AXIN2):c.2038_2039del (p.Thr680fs)
HGVS:
  • NC_000017.11:g.65536423_65536424del
  • NG_012142.1:g.30200_30201del
  • NM_001363813.1:c.1843_1844del
  • NM_004655.4:c.2038_2039delMANE SELECT
  • NP_001350742.1:p.Thr615fs
  • NP_004646.3:p.Thr680fs
  • LRG_296:g.30200_30201del
  • NC_000017.10:g.63532540_63532541del
  • NC_000017.10:g.63532541_63532542del
Protein change:
T615fs
Links:
dbSNP: rs2144441207
NCBI 1000 Genomes Browser:
rs2144441207
Molecular consequence:
  • NM_001363813.1:c.1843_1844del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004655.4:c.2038_2039del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Oligodontia-cancer predisposition syndrome
Synonyms:
TOOTH AGENESIS-COLORECTAL CANCER SYNDROME; Oligodontia-colorectal cancer syndrome
Identifiers:
MONDO: MONDO:0012075; MedGen: C1837750; Orphanet: 300576; OMIM: 608615

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002138646Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 8, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutations in AXIN2 cause familial tooth agenesis and predispose to colorectal cancer.

Lammi L, Arte S, Somer M, Jarvinen H, Lahermo P, Thesleff I, Pirinen S, Nieminen P.

Am J Hum Genet. 2004 May;74(5):1043-50. Epub 2004 Mar 23.

PubMed [citation]
PMID:
15042511
PMCID:
PMC1181967

AXIN2-associated autosomal dominant ectodermal dysplasia and neoplastic syndrome.

Marvin ML, Mazzoni SM, Herron CM, Edwards S, Gruber SB, Petty EM.

Am J Med Genet A. 2011 Apr;155A(4):898-902. doi: 10.1002/ajmg.a.33927. Epub 2011 Mar 17.

PubMed [citation]
PMID:
21416598
PMCID:
PMC3094478
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002138646.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1378845). This variant has not been reported in the literature in individuals affected with AXIN2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr680Profs*26) in the AXIN2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AXIN2 are known to be pathogenic (PMID: 15042511, 21416598).

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

Last Updated: Sep 29, 2024