NM_012330.4(KAT6B):c.3918del (p.Ile1307fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 16, 2016
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000391279.1

Allele description [Variation Report for NM_012330.4(KAT6B):c.3918del (p.Ile1307fs)]

NM_012330.4(KAT6B):c.3918del (p.Ile1307fs)

Gene:

KAT6B:lysine acetyltransferase 6B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q22.2

Genomic location:

Preferred name:

NM_012330.4(KAT6B):c.3918del (p.Ile1307fs)

HGVS:

NC_000010.11:g.75028742del
NG_032048.1:g.207330del
NM_001256468.2:c.3369del
NM_001256469.2:c.3042del
NM_001370132.1:c.2880del
NM_001370133.1:c.2229del
NM_001370134.1:c.1833del
NM_001370135.1:c.1575del
NM_001370136.1:c.3918del
NM_001370137.1:c.3918del
NM_001370138.1:c.3369del
NM_001370139.1:c.3042del
NM_001370140.1:c.3042del
NM_001370141.1:c.3042del
NM_001370142.1:c.3042del
NM_001370143.1:c.2853del
NM_001370144.1:c.2853del
NM_012330.4:c.3918delMANE SELECT
NP_001243397.1:p.Ile1124fs
NP_001243398.1:p.Ile1015fs
NP_001357061.1:p.Ile961fs
NP_001357062.1:p.Ile744fs
NP_001357063.1:p.Ile612fs
NP_001357064.1:p.Ile526fs
NP_001357065.1:p.Ile1307fs
NP_001357066.1:p.Ile1307fs
NP_001357067.1:p.Ile1124fs
NP_001357068.1:p.Ile1015fs
NP_001357069.1:p.Ile1015fs
NP_001357070.1:p.Ile1015fs
NP_001357071.1:p.Ile1015fs
NP_001357072.1:p.Ile952fs
NP_001357073.1:p.Ile952fs
NP_036462.2:p.Ile1307fs
NC_000010.10:g.76788500del
NM_012330.3:c.3918delG

Protein change:

I1015fs

Links:

dbSNP: rs886041987

NCBI 1000 Genomes Browser:

rs886041987

Molecular consequence:

NM_001256468.2:c.3369del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256469.2:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370132.1:c.2880del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370133.1:c.2229del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370134.1:c.1833del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370135.1:c.1575del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370136.1:c.3918del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370137.1:c.3918del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370138.1:c.3369del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370139.1:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370140.1:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370141.1:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370142.1:c.3042del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370143.1:c.2853del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370144.1:c.2853del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012330.4:c.3918del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000330805	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Sep 16, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000330805

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Sep 16, 2016)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000330805.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.3918delG variant in the KAT6B gene causes a frameshift starting with codon Isoleucine 1307, changes this amino acid to a Leucine residue and creates a premature Stop codon at position 27 of the new reading frame, denoted p.Ile1307LeufsX27. This variant is predicted to cause loss of normal protein function through protein truncation with the last 767 correct residues being replaced by 26 incorrect residues. Additionally, the variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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