NM_001348716.2(KDM6B):c.3046dup (p.Arg1016fs) AND Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 15, 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:: RCV002272591.3

Allele description [Variation Report for NM_001348716.2(KDM6B):c.3046dup (p.Arg1016fs)]

NM_001348716.2(KDM6B):c.3046dup (p.Arg1016fs)

Gene:

KDM6B:lysine demethylase 6B [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

17p13.1

Genomic location:

Preferred name:

NM_001348716.2(KDM6B):c.3046dup (p.Arg1016fs)

HGVS:

NC_000017.11:g.7849334dup
NG_053032.1:g.20135dup
NM_001080424.2:c.3046dup
NM_001348716.2:c.3046dupMANE SELECT
NP_001073893.1:p.Arg1016fs
NP_001335645.1:p.Arg1016fs
NC_000017.10:g.7752652dup
NM_001080424.2:c.3046dupC

Protein change:

R1016fs

Links:

dbSNP: rs2151378140

NCBI 1000 Genomes Browser:

rs2151378140

Molecular consequence:

NM_001080424.2:c.3046dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001348716.2:c.3046dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities
Synonyms:: STOLERMAN NEURODEVELOPMENTAL SYNDROME
Identifiers:: MONDO: MONDO:0032790; MedGen: C5193134; OMIM: 618505

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002556406	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 15, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002570473	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	no assertion criteria provided	Likely pathogenic (Sep 9, 2022)	de novo	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002556406

Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 15, 2022)

germline

clinical testing

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

SCV002570473

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

no assertion criteria provided

Likely pathogenic
(Sep 9, 2022)

de novo

research

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	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 Genetics and Molecular Pathology, SA Pathology, SCV002556406.2

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+, SCV002570473.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	not provided

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

Last Updated: Feb 20, 2024

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