VCV003257763.1 - ClinVar

NM_001291415.2(KDM6A):c.4073T>A (p.Leu1358Ter)

Germline

No data submitted for germline classification

Somatic

No data submitted for somatic clinical impact

Somatic

Oncogenicity

The aggregate oncogenicity classification for this variant for one or more tumor types, using the ClinGen/CGC/VICC terminology. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate oncogenicity classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely oncogenic

criteria provided, single submitter

Variant Details

Identifiers

NM_001291415.2(KDM6A):c.4073T>A (p.Leu1358Ter)

Variation ID: 3257763 Accession: VCV003257763.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xp11.3 X: 45107448 (GRCh38) [ NCBI UCSC ] X: 44966693 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Somatic - Oncogenicity	Aug 11, 2024	Aug 11, 2024	Jul 31, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001291415.2:c.4073T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001278344.1:p.Leu1358Ter	nonsense
NM_001291416.2:c.3938T>A	NP_001278345.1:p.Leu1313Ter	nonsense
NM_001291417.2:c.3782T>A	NP_001278346.1:p.Leu1261Ter	nonsense
NM_001291418.2:c.3680T>A	NP_001278347.1:p.Leu1227Ter	nonsense
NM_001291421.2:c.3029T>A	NP_001278350.1:p.Leu1010Ter	nonsense
NM_001410742.1:c.3815T>A	NP_001397671.1:p.Leu1272Ter	nonsense
NM_001419809.1:c.4181T>A	NP_001406738.1:p.Leu1394Ter	nonsense
NM_001419810.1:c.4079T>A	NP_001406739.1:p.Leu1360Ter	nonsense
NM_001419811.1:c.4046T>A	NP_001406740.1:p.Leu1349Ter	nonsense
NM_001419812.1:c.4025T>A	NP_001406741.1:p.Leu1342Ter	nonsense
NM_001419813.1:c.3971T>A	NP_001406742.1:p.Leu1324Ter	nonsense
NM_001419814.1:c.3923T>A	NP_001406743.1:p.Leu1308Ter	nonsense
NM_001419815.1:c.3788T>A	NP_001406744.1:p.Leu1263Ter	nonsense
NM_021140.4:c.3917T>A	NP_066963.2:p.Leu1306Ter	nonsense
NR_111960.2:n.4168T>A		non-coding transcript variant
NC_000023.11:g.45107448T>A
NC_000023.10:g.44966693T>A
NG_016260.1:g.239271T>A
LRG_616:g.239271T>A
LRG_616t1:c.4073T>A	LRG_616p1:p.Leu1358Ter

... more HGVS ... less HGVS

Protein change

L1358*, L1010*, L1263*, L1272*, L1313*, L1324*, L1342*, L1227*, L1308*, L1261*, L1306*, L1349*, L1360*, L1394*

Other names

Canonical SPDI

NC_000023.11:45107447:T:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
KDM6A		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	977	1175

Conditions - Somatic

Tumor type Help The tumor type for this variant-condition (RCV) record in ClinVar.	Clinical impact (# of submissions) Help The aggregate somatic clinical impact for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate somatic clinical impact is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status.	Oncogenicity Help The aggregate oncogenicity classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to the aggregate oncogenicity classification is shown in parentheses. The corresponding review status for the RCV record is indicated by stars. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the tumor type.	Variation/condition record Help The most recent date that a submitter evaluated this variant for the tumor type.
Neoplasm		Likely oncogenic criteria provided, single submitter	Jul 31, 2024	RCV004674078.1

Submissions - Somatic

Oncogenicity Help The submitted oncogenicity classification for each SCV record. (Last evaluated)	Review Status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Tumor type Help The tumor type for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the somatic clinical impact, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.

Likely oncogenic

(Jul 31, 2024)

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

Method: clinical testing

Neoplasm

Affected status: unknown

Allele origin: somatic

Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital

Accession: SCV005093898.1
First In ClinVar: Aug 11, 2024
Last updated: Aug 11, 2024

Citations for somatic classification of this variant

There are no citations for somatic classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Aug 11, 2024

ClinVar Genomic variation as it relates to human health

NM_001291415.2(KDM6A):c.4073T>A (p.Leu1358Ter)

Variant Details

Genes

Conditions - Somatic

Submissions - Somatic

Citations for somatic classification of this variant

Text-mined citations for this variant ...