NM_004655.4(AXIN2):c.1998C>A (p.Asn666Lys) AND Oligodontia-cancer predisposition syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 2023
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:: RCV001305287.4

Allele description

NM_004655.4(AXIN2):c.1998C>A (p.Asn666Lys)

Gene:

AXIN2:axin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q24.1

Genomic location:

Preferred name:

NM_004655.4(AXIN2):c.1998C>A (p.Asn666Lys)

HGVS:

NC_000017.11:g.65536463G>T
NG_012142.1:g.30160C>A
NM_001363813.1:c.1803C>A
NM_004655.4:c.1998C>AMANE SELECT
NP_001350742.1:p.Asn601Lys
NP_004646.3:p.Asn666Lys
LRG_296t1:c.1998C>A
LRG_296:g.30160C>A
NC_000017.10:g.63532581G>T
NM_004655.3:c.1998C>A

Protein change:

N601K

Links:

dbSNP: rs1460508423

NCBI 1000 Genomes Browser:

rs1460508423

Molecular consequence:

NM_001363813.1:c.1803C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004655.4:c.1998C>A - missense variant - [Sequence Ontology: SO:0001583]

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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Chain A, Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma...
Chain A, Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
gi|1111652225|pdb|5K6S|A

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001494616	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001494616

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2023)

germline

clinical testing

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

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

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001494616.4

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

Description

This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 666 of the AXIN2 protein (p.Asn666Lys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with AXIN2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1008015). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt AXIN2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: May 1, 2024

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