VCV002628338.2 - ClinVar

NM_012330.4(KAT6B):c.5646del (p.Asn1883fs)

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.

(2)

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, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_012330.4(KAT6B):c.5646del (p.Asn1883fs)

Variation ID: 2628338 Accession: VCV002628338.2

Type and length

Deletion, 1 bp

Location

Cytogenetic: 10q22.2 10: 75030465 (GRCh38) [ NCBI UCSC ] 10: 76790223 (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.
Germline	Nov 20, 2023	Sep 8, 2024	Apr 9, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_012330.4:c.5646del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_036462.2:p.Asn1883fs	frameshift
NM_001256468.2:c.5097del	NP_001243397.1:p.Asn1700fs	frameshift
NM_001256469.2:c.4770del	NP_001243398.1:p.Asn1591fs	frameshift
NM_001370132.1:c.4608del	NP_001357061.1:p.Asn1537fs	frameshift
NM_001370133.1:c.3957del	NP_001357062.1:p.Asn1320fs	frameshift
NM_001370134.1:c.3561del	NP_001357063.1:p.Asn1188fs	frameshift
NM_001370135.1:c.3303del	NP_001357064.1:p.Asn1102fs	frameshift
NM_001370136.1:c.5646del	NP_001357065.1:p.Asn1883fs	frameshift
NM_001370137.1:c.5646del	NP_001357066.1:p.Asn1883fs	frameshift
NM_001370138.1:c.5097del	NP_001357067.1:p.Asn1700fs	frameshift
NM_001370139.1:c.4770del	NP_001357068.1:p.Asn1591fs	frameshift
NM_001370140.1:c.4770del	NP_001357069.1:p.Asn1591fs	frameshift
NM_001370141.1:c.4770del	NP_001357070.1:p.Asn1591fs	frameshift
NM_001370142.1:c.4770del	NP_001357071.1:p.Asn1591fs	frameshift
NM_001370143.1:c.4581del	NP_001357072.1:p.Asn1528fs	frameshift
NM_001370144.1:c.4581del	NP_001357073.1:p.Asn1528fs	frameshift
NC_000010.11:g.75030470del
NC_000010.10:g.76790228del
NG_032048.1:g.209058del
NG_119859.1:g.446del

... more HGVS ... less HGVS

Protein change

N1102fs, N1188fs, N1320fs, N1528fs, N1537fs, N1591fs, N1700fs, N1883fs

Other names

Canonical SPDI

NC_000010.11:75030464:CCCCCC:CCCCC

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.
KAT6B		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh38 GRCh37	1285	1311

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.
Blepharophimosis - intellectual disability syndrome, SBBYS type	Pathogenic (1)	criteria provided, single submitter	Nov 10, 2023	RCV003397193.1
KAT6B-related disorder	Pathogenic (1)	criteria provided, single submitter	Apr 9, 2024	RCV004698882.1

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 (Nov 10, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Blepharophimosis - intellectual disability syndrome, SBBYS type Affected status: yes Allele origin: de novo	Daryl Scott Lab, Baylor College of Medicine Accession: SCV004102700.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023
Pathogenic (Apr 09, 2024)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	KAT6B-related disorder Affected status: yes Allele origin: germline	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center Accession: SCV005200920.1 First in ClinVar: Sep 08, 2024 Last updated: Sep 08, 2024	Comment: PVS1, PS2, PS4_Supporting, PM2

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.

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 Sep 08, 2024

ClinVar Genomic variation as it relates to human health

NM_012330.4(KAT6B):c.5646del (p.Asn1883fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...