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NM_000888.5(ITGB6):c.1661-3C>G AND Amelogenesis imperfecta type 1H

Germline classification:
Likely 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:
RCV001807870.2

Allele description [Variation Report for NM_000888.5(ITGB6):c.1661-3C>G]

NM_000888.5(ITGB6):c.1661-3C>G

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.1661-3C>G
HGVS:
  • NC_000002.12:g.160126604G>C
  • NG_042041.1:g.78710C>G
  • NM_000888.5:c.1661-3C>GMANE SELECT
  • NM_001282353.2:c.1661-3C>G
  • NM_001282354.2:c.1376-3C>G
  • NM_001282355.2:c.1660+10830C>G
  • NM_001282388.2:c.1535-3C>G
  • NM_001282389.2:c.1442-3C>G
  • NM_001282390.2:c.1247-3C>G
  • NC_000002.11:g.160983115G>C
Links:
dbSNP: rs1683256077
NCBI 1000 Genomes Browser:
rs1683256077
Molecular consequence:
  • NM_000888.5:c.1661-3C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282353.2:c.1661-3C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282354.2:c.1376-3C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282355.2:c.1660+10830C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282388.2:c.1535-3C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282389.2:c.1442-3C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001282390.2:c.1247-3C>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
2

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002058097Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicpaternal, germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Thaigermlineno1not providednot providednot providednot providedclinical testing
Thaipaternalyes1not providednot providednot providednot providedclinical 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, SCV002058097.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Thai1not providednot providedclinical testing PubMed (1)
2Thai1not providednot providedclinical testing PubMed (1)

Description

compound heterozygous with c.625G>T

Description

The heterozygous splice site variant c.1661-3C>G in ITGB6 (NM_000888.5) was identified in a patient with autosomal recessive amelogenesis imperfecta who also harbored heterozygous nonsense mutation c.625G>T p.(Gly209Ter). The c.1661-3C>G variant was inherited from his unaffected father and predicted to cause alteration to WT splice acceptor site. This variant was classified as likely pathogenic by ACMG guidelines.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot provided1not providednot providednot provided
2germlinenonot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 30, 2024