NM_005220.3(DLX3):c.574del (p.Glu192fs) AND multiple conditions

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 27, 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:: RCV000585754.2

Allele description [Variation Report for NM_005220.3(DLX3):c.574del (p.Glu192fs)]

NM_005220.3(DLX3):c.574del (p.Glu192fs)

Gene:

DLX3:distal-less homeobox 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

17q21.33

Genomic location:

Preferred name:

NM_005220.3(DLX3):c.574del (p.Glu192fs)

HGVS:

NC_000017.11:g.49991810del
NG_023063.1:g.8418del
NM_005220.3:c.574delMANE SELECT
NP_005211.1:p.Glu192fs
NC_000017.10:g.48069174del
NM_005220.2:c.574delG

Protein change:

E192fs

Links:

dbSNP: rs1057518764

NCBI 1000 Genomes Browser:

rs1057518764

Molecular consequence:

NM_005220.3:c.574del - frameshift variant - [Sequence Ontology: SO:0001589]

Functional consequence:

functional variant [Sequence Ontology: SO:0001536]

Condition(s)

Name:: Hypomaturation-hypoplastic amelogenesis imperfecta with taurodontism
Synonyms:: Amelogenesis imperfecta, type IV
Identifiers:: MONDO: MONDO:0007093; MedGen: C1863012; Orphanet: 88661; OMIM: 104510

Name:: Tricho-dento-osseous syndrome (TDO)
Synonyms:: TDO syndrome; Enamel hypoplasia and hypocalcification with associated strikingly curly hair
Identifiers:: MONDO: MONDO:0008592; MedGen: C0265333; Orphanet: 3352; OMIM: 190320

Recent activity

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Signal recognition particle, SRP9/SRP14 subunit [Arabidopsis thaliana]
Signal recognition particle, SRP9/SRP14 subunit [Arabidopsis thaliana]
Gene ID:824071

Gene
At.35648 AND (alive[prop]) (1)
Gene
ADF2 actin depolymerizing factor 2 [Arabidopsis thaliana]
ADF2 actin depolymerizing factor 2 [Arabidopsis thaliana]
Gene ID:823743

Gene
At.20461 AND (alive[prop]) (1)
Gene
beta-N-acetylhexosaminidase [Priestia megaterium]
beta-N-acetylhexosaminidase [Priestia megaterium]
gi|1830455565|gnl|PRJNA622823|HFZ78 5|gb|QIZ10344.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000583455	Leeds Amelogenesis Imperfecta Research Group, University of Leeds	no assertion criteria provided	Pathogenic (Jul 3, 2017)	germline	research
SCV002787045	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 27, 2022)	unknown	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

SCV000583455

Leeds Amelogenesis Imperfecta Research Group, University of Leeds

no assertion criteria provided

Pathogenic
(Jul 3, 2017)

germline

research

SCV002787045

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 27, 2022)

unknown

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
Mixed race: Afro-caribbean / White British	germline	yes	5	1	not provided	not provided	not provided	research

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 Leeds Amelogenesis Imperfecta Research Group, University of Leeds, SCV000583455.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	Mixed race: Afro-caribbean / White British	5	not provided	not provided	research	not provided

Description

The frameshift variant is within the final exon and therefore the protein is likely to escape nonsense mediated decay. The final 96 amino acids are expected to be lost from the 287 amino acid protein.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		5	not provided	1	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002787045.1

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

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

Last Updated: Jan 7, 2023

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