VCV001342507.2 - ClinVar

NC_000007.14:g.152052676_152295696del

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. 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 germline 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.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000007.14:g.152052676_152295696del

Variation ID: 1342507 Accession: VCV001342507.2

Type and length

Deletion, 243,021 bp

Location

Cytogenetic: 7q36.1 7: 152052676-152295696 (GRCh38) [ 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.
Germline	Feb 26, 2022	Oct 7, 2023	Apr 13, 2021

HGVS

Nucleotide	Protein	Molecular consequence
NC_000007.14:g.152052676_152295696del

Protein change

Other names

Canonical SPDI

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.
KMT2C		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	1757	1908
GALNT11		-	-	GRCh38 GRCh37	32	145
LOC123956272	-	-	-	GRCh38	-	61
LOC126860227	-	-	-	GRCh38	-	50
LOC129389938	-	-	-	GRCh38	-	46
LOC129999675	-	-	-	GRCh38	-	56

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Kleefstra syndrome 2	Pathogenic (1)	criteria provided, single submitter	Apr 13, 2021	RCV001839258.1

Submissions - Germline

Classification Help The submitted germline 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)	Condition Help The condition 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 classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Apr 13, 2021)	criteria provided, single submitter (NYGC Assertion Criteria 2020) Method: clinical testing	Kleefstra syndrome 2 Affected status: unknown Allele origin: de novo	New York Genome Center Study: CSER-NYCKidSeq Accession: SCV002099230.2 First in ClinVar: Feb 26, 2022 Last updated: Oct 07, 2023	Comment: The de novo ~243kb deletion deletes the last 53 exons (exon 7-59) of the KMT2C gene. The majority of pathogenic variants in KMT2C are nonsense … (more) The de novo ~243kb deletion deletes the last 53 exons (exon 7-59) of the KMT2C gene. The majority of pathogenic variants in KMT2C are nonsense or frameshift [PMID: 29069077; PMID: 32366967], suggesting loss-of-function is the likely mechanism of the disease. ClinGen Dosage Sensitivity curation [https://search.clinicalgenome.org/kb/gene-dosage/HGNC:13726] indicates that the KMT2C gene has a haploinsufficiency score of 3 (i.e.,sufficient evidence for haploinsufficiency). Based on the available evidence, this de novo ~243kb deletion is classified as pathogenic. (less) Number of individuals with the variant: 1 Clinical Features: Seizure (present) , Intellectual disability (present) , Autism (present) Secondary finding: no

Comment:

The de novo ~243kb deletion deletes the last 53 exons (exon 7-59) of the KMT2C gene. The majority of pathogenic variants in KMT2C are nonsense or frameshift [PMID: 29069077; PMID: 32366967], suggesting loss-of-function is the likely mechanism of the disease. ClinGen Dosage Sensitivity curation [https://search.clinicalgenome.org/kb/gene-dosage/HGNC:13726] indicates that the KMT2C gene has a haploinsufficiency score of 3 (i.e.,sufficient evidence for haploinsufficiency). Based on the available evidence, this de novo ~243kb deletion is classified as pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline 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 Oct 15, 2023

ClinVar Genomic variation as it relates to human health

NC_000007.14:g.152052676_152295696del

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...