NM_001291415.2(KDM6A):c.593dup (p.Asn198fs) AND Neoplasm

Germline classification:: None
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:: Likely oncogenic (1 submission)
Last evaluated:: Jul 31, 2024
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Record status:: current
Accession:: RCV004666444.1

Allele description [Variation Report for NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)]

NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)

Gene:

KDM6A:lysine demethylase 6A [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

Xp11.3

Genomic location:

Preferred name:

NM_001291415.2(KDM6A):c.593dup (p.Asn198fs)

HGVS:

NC_000023.11:g.45034959dup
NG_016260.1:g.166782dup
NM_001291415.2:c.593dupMANE SELECT
NM_001291416.2:c.593dup
NM_001291417.2:c.593dup
NM_001291418.2:c.593dup
NM_001291421.2:c.-161dup
NM_001410742.1:c.593dup
NM_001419809.1:c.593dup
NM_001419810.1:c.593dup
NM_001419811.1:c.593dup
NM_001419812.1:c.593dup
NM_001419813.1:c.593dup
NM_001419814.1:c.593dup
NM_001419815.1:c.593dup
NM_021140.4:c.593dup
NP_001278344.1:p.Asn198Lysfs
NP_001278344.1:p.Asn198fs
NP_001278345.1:p.Asn198fs
NP_001278346.1:p.Asn198fs
NP_001278347.1:p.Asn198fs
NP_001397671.1:p.Asn198fs
NP_001406738.1:p.Asn198fs
NP_001406739.1:p.Asn198fs
NP_001406740.1:p.Asn198fs
NP_001406741.1:p.Asn198fs
NP_001406742.1:p.Asn198fs
NP_001406743.1:p.Asn198fs
NP_001406744.1:p.Asn198fs
NP_066963.2:p.Asn198fs
LRG_616t1:c.593dup
LRG_616:g.166782dup
LRG_616p1:p.Asn198Lysfs
NC_000023.10:g.44894204dup
NM_001291415.1:c.593dup
NM_021140.4:c.593dupA
NR_111960.2:n.957dup

Protein change:

N198fs

Molecular consequence:

NM_001291421.2:c.-161dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001291415.2:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291416.2:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291417.2:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001291418.2:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001410742.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419809.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419810.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419811.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419812.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419813.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419814.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001419815.1:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_021140.4:c.593dup - frameshift variant - [Sequence Ontology: SO:0001589]
NR_111960.2:n.957dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Neoplasm
Synonyms:: Neoplasms; Neoplasm (disease)
Identifiers:: MONDO: MONDO:0005070; MeSH: D009369; MedGen: C0027651; Human Phenotype Ontology: HP:0002664

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005094041	Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	criteria provided, single submitter (ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022)	Likely oncogenic (Jul 31, 2024)	somatic	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

SCV005094041

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

criteria provided, single submitter

(ClinGen/CGC/VICC Guidelines for Oncogenicity, 2022)

Likely oncogenic
(Jul 31, 2024)

somatic

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

Citations

PubMed

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC).

Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, et al.

Genet Med. 2022 May;24(5):986-998. doi: 10.1016/j.gim.2022.01.001. Epub 2022 Jan 29. Erratum in: Genet Med. 2022 Sep;24(9):1991. doi: 10.1016/j.gim.2022.07.001.

PubMed [citation]

PMID:: 35101336
PMCID:: PMC9081216

Details of each submission

From Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, SCV005094041.1

#	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	somatic	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 11, 2024

ClinVar

Relating variation to medicine