NM_203486.3(DLL3):c.712C>T (p.Arg238Ter) AND Spondylocostal dysostosis 1, autosomal recessive

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 5, 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:: RCV000007235.5

Allele description [Variation Report for NM_203486.3(DLL3):c.712C>T (p.Arg238Ter)]

NM_203486.3(DLL3):c.712C>T (p.Arg238Ter)

Gene:

DLL3:delta like canonical Notch ligand 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_203486.3(DLL3):c.712C>T (p.Arg238Ter)

HGVS:

NC_000019.10:g.39504130C>T
NG_008256.1:g.10214C>T
NM_016941.4:c.712C>T
NM_203486.3:c.712C>TMANE SELECT
NP_058637.1:p.Arg238Ter
NP_982353.1:p.Arg238Ter
NC_000019.9:g.39994770C>T
NM_016941.3:c.712C>T

Protein change:

R238*; ARG238TER

Links:

OMIM: 602768.0006; dbSNP: rs104894675

NCBI 1000 Genomes Browser:

rs104894675

Molecular consequence:

NM_016941.4:c.712C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_203486.3:c.712C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Spondylocostal dysostosis 1, autosomal recessive (SCDO1)
Identifiers:: MONDO: MONDO:0020692; MedGen: CN032975; Orphanet: 2311; OMIM: 277300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027431	OMIM	no assertion criteria provided	Pathogenic (Jul 1, 2003)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV004040808	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 5, 2023)	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

SCV000027431

OMIM

no assertion criteria provided

Pathogenic
(Jul 1, 2003)

germline

literature only

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

SCV004040808

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(May 5, 2023)

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
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

A cluster of autosomal recessive spondylocostal dysostosis caused by three newly identified DLL3 mutations segregating in a small village.

Bonafé L, Giunta C, Gassner M, Steinmann B, Superti-Furga A.

Clin Genet. 2003 Jul;64(1):28-35.

PubMed [citation]

PMID:: 12791036

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 OMIM, SCV000027431.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

For discussion of the arg238-to-ter (R238X) mutation in the DLL3 gene that was found in compound heterozygous state in affected individuals from Switzerland with spondylocostal dysostosis (SCDO1; 277300) by Bonafe et al. (2003), see 602768.0004.

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

From Baylor Genetics, SCV004040808.1

#	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: Sep 29, 2024

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