NM_012330.4(KAT6B):c.3246del (p.Glu1083fs) AND Blepharophimosis - intellectual disability syndrome, SBBYS type - ClinVar

NM_012330.4(KAT6B):c.3246del (p.Glu1083fs) AND Blepharophimosis - intellectual disability syndrome, SBBYS type

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003338008.2

Allele description [Variation Report for NM_012330.4(KAT6B):c.3246del (p.Glu1083fs)]

NM_012330.4(KAT6B):c.3246del (p.Glu1083fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

10q22.2

Genomic location:

Preferred name:

NM_012330.4(KAT6B):c.3246del (p.Glu1083fs)

HGVS:

NC_000010.11:g.75022105del
NG_032048.1:g.200693del
NM_001256468.2:c.2697del
NM_001256469.2:c.2370del
NM_001370132.1:c.2208del
NM_001370133.1:c.1557del
NM_001370134.1:c.1161del
NM_001370135.1:c.903del
NM_001370136.1:c.3246del
NM_001370137.1:c.3246del
NM_001370138.1:c.2697del
NM_001370139.1:c.2370del
NM_001370140.1:c.2370del
NM_001370141.1:c.2370del
NM_001370142.1:c.2370del
NM_001370143.1:c.2181del
NM_001370144.1:c.2181del
NM_012330.4:c.3246delMANE SELECT
NP_001243397.1:p.Glu900fs
NP_001243398.1:p.Glu791fs
NP_001357061.1:p.Glu737fs
NP_001357062.1:p.Glu520fs
NP_001357063.1:p.Glu388fs
NP_001357064.1:p.Glu302fs
NP_001357065.1:p.Glu1083fs
NP_001357066.1:p.Glu1083fs
NP_001357067.1:p.Glu900fs
NP_001357068.1:p.Glu791fs
NP_001357069.1:p.Glu791fs
NP_001357070.1:p.Glu791fs
NP_001357071.1:p.Glu791fs
NP_001357072.1:p.Glu728fs
NP_001357073.1:p.Glu728fs
NP_036462.2:p.Glu1083fs
NC_000010.10:g.76781863del

Protein change:

E1083fs

Molecular consequence:

NM_001256468.2:c.2697del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001256469.2:c.2370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370132.1:c.2208del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370133.1:c.1557del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370134.1:c.1161del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370135.1:c.903del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370136.1:c.3246del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370137.1:c.3246del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370138.1:c.2697del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370139.1:c.2370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370140.1:c.2370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370141.1:c.2370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370142.1:c.2370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370143.1:c.2181del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001370144.1:c.2181del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_012330.4:c.3246del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Blepharophimosis - intellectual disability syndrome, SBBYS type (SBBYSS)
Synonyms:: OHDO SYNDROME, SBBYS VARIANT; Young Simpson syndrome; Mental retardation unusual facies hypothyroidism; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011365; MedGen: C1863557; Orphanet: 3047; OMIM: 603736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004048520	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004048520

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004048520.1

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

Description

The frame shift variant c.3246del (p.Glu1083ArgfsTer31) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Glu1083ArgfsTer31 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant causes a frameshift starting with codon Glutamic Acid 1083, changes this amino acid to Arginine residue, and creates a premature Stop codon at position 31 of the new reading frame, denoted p.Glu1083ArgfsTer31. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

#	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: Apr 6, 2024

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