NM_000888.5(ITGB6):c.625G>T (p.Gly209Ter) AND Amelogenesis imperfecta type 1H

Germline classification:: Pathogenic (1 submission)
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:: RCV001807869.2

Allele description [Variation Report for NM_000888.5(ITGB6):c.625G>T (p.Gly209Ter)]

NM_000888.5(ITGB6):c.625G>T (p.Gly209Ter)

Gene:

ITGB6:integrin subunit beta 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q24.2

Genomic location:

Preferred name:

NM_000888.5(ITGB6):c.625G>T (p.Gly209Ter)

HGVS:

NC_000002.12:g.160174108C>A
NG_042041.1:g.31206G>T
NM_000888.5:c.625G>TMANE SELECT
NM_001282353.2:c.625G>T
NM_001282354.2:c.340G>T
NM_001282355.2:c.625G>T
NM_001282388.2:c.499G>T
NM_001282389.2:c.406G>T
NM_001282390.2:c.211G>T
NP_000879.2:p.Gly209Ter
NP_001269282.1:p.Gly209Ter
NP_001269283.1:p.Gly114Ter
NP_001269284.1:p.Gly209Ter
NP_001269317.1:p.Gly167Ter
NP_001269318.1:p.Gly136Ter
NP_001269319.1:p.Gly71Ter
NC_000002.11:g.161030619C>A

Protein change:

G114*

Links:

dbSNP: rs561588576

NCBI 1000 Genomes Browser:

rs561588576

Molecular consequence:

NM_000888.5:c.625G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282353.2:c.625G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282354.2:c.340G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282355.2:c.625G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282388.2:c.499G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282389.2:c.406G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001282390.2:c.211G>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Amelogenesis imperfecta type 1H
Synonyms:: Amelogenesis imperfecta, type IH
Identifiers:: MONDO: MONDO:0014540; MedGen: C4015557; Orphanet: 88661; OMIM: 616221

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002058096	Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	maternal, 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

SCV002058096

Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

maternal, 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
Thai	germline	no	1	not provided	not provided	not provided	not provided	clinical testing
Thai	maternal	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University, SCV002058096.1

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

Description

compound heterozygous with c.1661-3C>G

Description

The heterozygous nonsense mutation c.625G>T p.(Gly209Ter) in ITGB6 (NM_000888.5) was identified in a patient with autosomal recessive amelogenesis imperfecta who also harbored heterozygous splice site variant c.1661-3C>G. A homozygous nonsense mutation in ITGB6 was previously reported in a patient with with hypoplastic amelogenesis imperfecta (Wang el al., 2014). This variant was classified as pathogenic by ACMG guidelines.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided
2	germline	no	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Mar 30, 2024

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