NM_001372076.1(PAX9):c.259A>T (p.Ile87Phe) AND Partial congenital absence of teeth

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 25, 2018
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:: RCV000704798.8

Allele description [Variation Report for NM_001372076.1(PAX9):c.259A>T (p.Ile87Phe)]

NM_001372076.1(PAX9):c.259A>T (p.Ile87Phe)

Gene:

PAX9:paired box 9 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q13.3

Genomic location:

Preferred name:

NM_001372076.1(PAX9):c.259A>T (p.Ile87Phe)

HGVS:

NC_000014.9:g.36663151A>T
NG_013357.1:g.10584A>T
NM_001372076.1:c.259A>TMANE SELECT
NM_006194.4:c.259A>T
NP_001359005.1:p.Ile87Phe
NP_006185.1:p.Ile87Phe
NP_006185.1:p.Ile87Phe
NC_000014.8:g.37132356A>T
NM_006194.3:c.259A>T

Protein change:

I87F; ILE87PHE

Links:

OMIM: 167416.0009; dbSNP: rs104894468

NCBI 1000 Genomes Browser:

rs104894468

Molecular consequence:

NM_001372076.1:c.259A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_006194.4:c.259A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Partial congenital absence of teeth
Synonyms:: TOOTH AGENESIS, FAMILIAL; Tooth agenesis, selective; Hypodontia
Identifiers:: MONDO: MONDO:0005486; MedGen: C0020608; OMIM: PS106600; Human Phenotype Ontology: HP:0000668

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000833765	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 25, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16479262, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000833765

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 25, 2018)

germline

clinical testing

PubMed (2)
[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

Molecular characterization of a novel PAX9 missense mutation causing posterior tooth agenesis.

Kapadia H, Frazier-Bowers S, Ogawa T, D'Souza RN.

Eur J Hum Genet. 2006 Apr;14(4):403-9.

PubMed [citation]

PMID:: 16479262

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000833765.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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. Experimental studies have shown that this missense change impairs protein stability and DNA binding activities of the PAX9 protien (PMID: 16479262). This variant has been observed to segregate with oligodontia in one family (PMID: 16479262). ClinVar contains an entry for this variant (Variation ID: 13775). This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with phenylalanine at codon 87 of the PAX9 protein (p.Ile87Phe). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and phenylalanine.

#	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

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