NM_016604.4(KDM3B):c.277G>T (p.Glu93Ter) AND Diets-Jongmans syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 22, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001072132.3

Allele description [Variation Report for NM_016604.4(KDM3B):c.277G>T (p.Glu93Ter)]

NM_016604.4(KDM3B):c.277G>T (p.Glu93Ter)

Gene:

KDM3B:lysine demethylase 3B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q31.2

Genomic location:

Preferred name:

NM_016604.4(KDM3B):c.277G>T (p.Glu93Ter)

HGVS:

NC_000005.10:g.138372758G>T
NM_016604.4:c.277G>TMANE SELECT
NP_057688.3:p.Glu93Ter
NC_000005.9:g.137708447G>T
NM_016604.3:c.277G>T

Protein change:

E93*; GLU93TER

Links:

OMIM: 609373.0001; dbSNP: rs1761904420

NCBI 1000 Genomes Browser:

rs1761904420

Molecular consequence:

NM_016604.4:c.277G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Diets-Jongmans syndrome
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER WITH DISTINCTIVE FACIAL DYSMORPHISM
Identifiers:: MONDO: MONDO:0030012; MedGen: C5394263; OMIM: 618846

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001237475	OMIM	no assertion criteria provided	Pathogenic (Jan 22, 2021)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 30929739, 29351919 Hamosh, A. Personal Communication. 2020. Baltimore, Md.

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001237475

OMIM

no assertion criteria provided

Pathogenic
(Jan 22, 2021)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

Hamosh, A. Personal Communication. 2020. Baltimore, Md.

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

De Novo and Inherited Pathogenic Variants in KDM3B Cause Intellectual Disability, Short Stature, and Facial Dysmorphism.

Diets IJ, van der Donk R, Baltrunaite K, Waanders E, Reijnders MRF, Dingemans AJM, Pfundt R, Vulto-van Silfhout AT, Wiel L, Gilissen C, Thevenon J, Perrin L, Afenjar A, Nava C, Keren B, Bartz S, Peri B, Beunders G, Verbeek N, van Gassen K, Thiffault I, Cadieux-Dion M, et al.

Am J Hum Genet. 2019 Apr 4;104(4):758-766. doi: 10.1016/j.ajhg.2019.02.023. Epub 2019 Mar 28.

PubMed [citation]

PMID:: 30929739
PMCID:: PMC6451728

High Yield of Pathogenic Germline Mutations Causative or Likely Causative of the Cancer Phenotype in Selected Children with Cancer.

Diets IJ, Waanders E, Ligtenberg MJ, van Bladel DAG, Kamping EJ, Hoogerbrugge PM, Hopman S, Olderode-Berends MJ, Gerkes EH, Koolen DA, Marcelis C, Santen GW, van Belzen MJ, Mordaunt D, McGregor L, Thompson E, Kattamis A, Pastorczak A, Mlynarski W, Ilencikova D, van Silfhout AV, Gardeitchik T, et al.

Clin Cancer Res. 2018 Apr 1;24(7):1594-1603. doi: 10.1158/1078-0432.CCR-17-1725. Epub 2018 Jan 19.

PubMed [citation]

PMID:: 29351919

Details of each submission

From OMIM, SCV001237475.2

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

Description

In a 16-year-old female (patient 2) with Diets-Jongmans syndrome (DIJOS; 618846), Diets et al. (2019) reported a G-to-T transversion (c.277G-T, NM_016604.3) at nucleotide 277 of the KDM3B gene resulting in a glu-to-ter codon substitution at amino acid 93 (E93X). This change was inherited from her affected mother (patient 3). The proband also had variants of uncertain significance in BAP1 (I706V) and CHD7 (R886Q) that were absent in her mother. This patient had been reported by Diets et al. (2018) (patient 33) due to her acute myeloid leukemia. This variant was not present in the gnomAD database (April 14, 2020) (Hamosh, 2020).

#	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

Last Updated: Apr 23, 2022

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