VCV000260238.39 - ClinVar

NM_012330.4(KAT6B):c.3289GAA[9] (p.Glu1104dup)

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.

(8)

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.

Benign/Likely benign

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.3289GAA[9] (p.Glu1104dup)

Variation ID: 260238 Accession: VCV000260238.39

Type and length

Microsatellite, 3 bp

Location

Cytogenetic: 10q22.2 10: 75022147-75022148 (GRCh38) [ NCBI UCSC ] 10: 76781905-76781906 (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	Oct 3, 2016	Oct 20, 2024	Aug 1, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_012330.4:c.3289GAA[9] MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_036462.2:p.Glu1104dup	inframe insertion
NM_001256468.2:c.2740GAA[9]	NP_001243397.1:p.Glu921dup	inframe insertion
NM_001256469.2:c.2413GAA[9]	NP_001243398.1:p.Glu812dup	inframe insertion
NM_001370132.1:c.2251GAA[9]	NP_001357061.1:p.Glu758dup	inframe insertion
NM_001370133.1:c.1600GAA[9]	NP_001357062.1:p.Glu541dup	inframe insertion
NM_001370134.1:c.1204GAA[9]	NP_001357063.1:p.Glu409dup	inframe insertion
NM_001370135.1:c.946GAA[9]	NP_001357064.1:p.Glu323dup	inframe insertion
NM_001370136.1:c.3289GAA[9]	NP_001357065.1:p.Glu1104dup	inframe insertion
NM_001370137.1:c.3289GAA[9]	NP_001357066.1:p.Glu1104dup	inframe insertion
NM_001370138.1:c.2740GAA[9]	NP_001357067.1:p.Glu921dup	inframe insertion
NM_001370139.1:c.2413GAA[9]	NP_001357068.1:p.Glu812dup	inframe insertion
NM_001370140.1:c.2413GAA[9]	NP_001357069.1:p.Glu812dup	inframe insertion
NM_001370141.1:c.2413GAA[9]	NP_001357070.1:p.Glu812dup	inframe insertion
NM_001370142.1:c.2413GAA[9]	NP_001357071.1:p.Glu812dup	inframe insertion
NM_001370143.1:c.2224GAA[9]	NP_001357072.1:p.Glu749dup	inframe insertion
NM_001370144.1:c.2224GAA[9]	NP_001357073.1:p.Glu749dup	inframe insertion
NM_012330.3:c.3310_3312dup
NC_000010.11:g.75022148GAA[9]
NC_000010.10:g.76781906GAA[9]
NG_032048.1:g.200736GAA[9]

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000010.11:75022147:GAAGAAGAAGAAGAAGAAGAAGAA:GAAGAAGAAGAAGAAGAAGAAGAAGAA

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.

0.45968 (GAAGAAGAAGAAGAAGAAGAA)

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

Links

ClinGen: CA5564784 dbSNP: rs71929101 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	1281	1307

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.
not specified	Benign/Likely benign (3)	criteria provided, multiple submitters, no conflicts	Aug 28, 2017	RCV000246745.13
Genitopatellar syndrome	Likely benign (1)	criteria provided, single submitter	Jan 30, 2024	RCV001033983.11
not provided	Benign (4)	criteria provided, multiple submitters, no conflicts	Aug 1, 2024	RCV001529580.19

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.
Benign (Aug 28, 2017)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Not Specified Affected status: unknown Allele origin: germline	Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital Accession: SCV000864360.1 First in ClinVar: Jan 22, 2019 Last updated: Jan 22, 2019	Comment: BS1, BS2, BP3; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where … (more) BS1, BS2, BP3; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and is an in-frame deletion/insertion in a repetitive region without a known function. (less)
Likely benign (Jan 30, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Genitopatellar syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV001197307.6 First in ClinVar: Apr 15, 2020 Last updated: Feb 20, 2024
Likely benign (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	NOT SPECIFIED Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV000311909.1 First in ClinVar: Oct 03, 2016 Last updated: Oct 03, 2016
Benign (Dec 21, 2016)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV001873383.1 First in ClinVar: Sep 19, 2021 Last updated: Sep 19, 2021
Benign (Aug 01, 2024)	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2) Method: clinical testing	not provided Affected status: yes Allele origin: germline	CeGaT Center for Human Genetics Tuebingen Accession: SCV002821518.14 First in ClinVar: Jan 21, 2023 Last updated: Oct 20, 2024	Comment: KAT6B: BS1, BS2 Number of individuals with the variant: 13
Likely benign (-)	no assertion criteria provided Method: clinical testing	not provided Affected status: yes Allele origin: germline	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001743248.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021
Likely benign (-)	no assertion criteria provided Method: clinical testing	not provided Affected status: yes Allele origin: germline	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) Study: VKGL Data-share Consensus Accession: SCV001800184.1 First in ClinVar: Aug 21, 2021 Last updated: Aug 21, 2021
Benign (-)	no assertion criteria provided Method: clinical testing	not specified Affected status: yes Allele origin: germline	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center Additional submitter: Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen Study: VKGL Data-share Consensus Accession: SCV001965923.1 First in ClinVar: Oct 07, 2021 Last updated: Oct 07, 2021

Comment:

BS1, BS2, BP3; This alteration has an allele frequency that is greater than expected for the associated disease, was seen in a healthy adult where full penetrance of the disorder is expected at an early age, and is an in-frame deletion/insertion in a repetitive region without a known function.

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 rs71929101 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 20, 2024

ClinVar Genomic variation as it relates to human health

NM_012330.4(KAT6B):c.3289GAA[9] (p.Glu1104dup)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs71929101 ...