NM_004655.4(AXIN2):c.1929_1935del (p.Tyr644fs) AND Oligodontia-cancer predisposition syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 3, 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:: RCV002886149.3

Allele description [Variation Report for NM_004655.4(AXIN2):c.1929_1935del (p.Tyr644fs)]

NM_004655.4(AXIN2):c.1929_1935del (p.Tyr644fs)

Gene:

AXIN2:axin 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q24.1

Genomic location:

Preferred name:

NM_004655.4(AXIN2):c.1929_1935del (p.Tyr644fs)

HGVS:

NC_000017.11:g.65536527_65536533del
NG_012142.1:g.30091_30097del
NM_001363813.1:c.1734_1740del
NM_004655.4:c.1929_1935delMANE SELECT
NP_001350742.1:p.Tyr579fs
NP_004646.3:p.Tyr644Trpfs
NP_004646.3:p.Tyr644fs
LRG_296t1:c.1928_1934del
LRG_296:g.30091_30097del
LRG_296p1:p.Tyr644Trpfs
NC_000017.10:g.63532644_63532650del
NC_000017.10:g.63532645_63532651del
NM_004655.3:c.1928_1934delCCTACCC

Protein change:

Y579fs

Molecular consequence:

NM_001363813.1:c.1734_1740del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004655.4:c.1929_1935del - 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

Recent activity

Clear Turn Off Turn On

atos homolog protein B [Homo sapiens]
atos homolog protein B [Homo sapiens]
gi|33636717|ref|NP_079458.2|

Protein
Homo sapiens zinc finger CCCH-type containing 7A, mRNA (cDNA clone IMAGE:5527491...
Homo sapiens zinc finger CCCH-type containing 7A, mRNA (cDNA clone IMAGE:5527491), partial cds
gi|22477676|gb|BC036857.1|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003245607	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 3, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15042511, 21416598, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003245607

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 3, 2022)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV003245607.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. 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.Tyr644Trpfs*43) 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).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine