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NM_012330.4(KAT6B):c.3690_3699del (p.Asn1230fs) AND Genitopatellar syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jan 25, 2023
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:
RCV002789988.3

Allele description [Variation Report for NM_012330.4(KAT6B):c.3690_3699del (p.Asn1230fs)]

NM_012330.4(KAT6B):c.3690_3699del (p.Asn1230fs)

Gene:
KAT6B:lysine acetyltransferase 6B [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q22.2
Genomic location:
Preferred name:
NM_012330.4(KAT6B):c.3690_3699del (p.Asn1230fs)
Other names:
NM_001256469.2:c.2814_2823del
HGVS:
  • NC_000010.11:g.75028514_75028523del
  • NG_032048.1:g.207102_207111del
  • NM_001256468.2:c.3141_3150del
  • NM_001256469.2:c.2814_2823del
  • NM_001370132.1:c.2652_2661del
  • NM_001370133.1:c.2001_2010del
  • NM_001370134.1:c.1605_1614del
  • NM_001370135.1:c.1347_1356del
  • NM_001370136.1:c.3690_3699del
  • NM_001370137.1:c.3690_3699del
  • NM_001370138.1:c.3141_3150del
  • NM_001370139.1:c.2814_2823del
  • NM_001370140.1:c.2814_2823del
  • NM_001370141.1:c.2814_2823del
  • NM_001370142.1:c.2814_2823del
  • NM_001370143.1:c.2625_2634del
  • NM_001370144.1:c.2625_2634del
  • NM_012330.4:c.3690_3699delMANE SELECT
  • NP_001243397.1:p.Asn1047fs
  • NP_001243398.1:p.Asn938fs
  • NP_001357061.1:p.Asn884fs
  • NP_001357062.1:p.Asn667fs
  • NP_001357063.1:p.Asn535fs
  • NP_001357064.1:p.Asn449fs
  • NP_001357065.1:p.Asn1230fs
  • NP_001357066.1:p.Asn1230fs
  • NP_001357067.1:p.Asn1047fs
  • NP_001357068.1:p.Asn938fs
  • NP_001357069.1:p.Asn938fs
  • NP_001357070.1:p.Asn938fs
  • NP_001357071.1:p.Asn938fs
  • NP_001357072.1:p.Asn875fs
  • NP_001357073.1:p.Asn875fs
  • NP_036462.2:p.Asn1230fs
  • NC_000010.10:g.76788272_76788281del
Protein change:
N1047fs
Molecular consequence:
  • NM_001256468.2:c.3141_3150del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001256469.2:c.2814_2823del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370132.1:c.2652_2661del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370133.1:c.2001_2010del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370134.1:c.1605_1614del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370135.1:c.1347_1356del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370136.1:c.3690_3699del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370137.1:c.3690_3699del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370138.1:c.3141_3150del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370139.1:c.2814_2823del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370140.1:c.2814_2823del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370141.1:c.2814_2823del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370142.1:c.2814_2823del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370143.1:c.2625_2634del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370144.1:c.2625_2634del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012330.4:c.3690_3699del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Genitopatellar syndrome (GTPTS)
Synonyms:
ABSENT PATELLAE, SCROTAL HYPOPLASIA, RENAL ANOMALIES, FACIAL DYSMORPHISM, AND MENTAL RETARDATION
Identifiers:
MONDO: MONDO:0011640; MedGen: C1853566; Orphanet: 85201; OMIM: 606170

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003761289Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Jan 25, 2023) 		germlinecuration

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

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 Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV003761289.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

The heterozygous p.Asn1230LysfsTer10 variant in KAT6B was identified by our study in one individual with agenesis of the corpus callosum, global developmental delay, and seizure. Trio exome analysis showed this variant to be de novo. The p.Asn1230LysfsTer10 variant in KAT6B has not been previously reported in individuals with genitopatellar syndrome. This variant was absent from large population studies. This variant is predicted to cause a frameshift, which alters the protein’s amino acid sequence beginning at position 1230 and leads to a premature termination codon 10 amino acids downstream. This termination codon occurs within the terminal 50 bases of the last exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Heterozygous loss of function of the KAT6B gene is an established disease mechanism in autosomal dominant genitopatellar syndrome. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive congenital myasthenic syndrome 19. ACMG/AMP Criteria applied: PVS1_Strong, PS2_Supporting, PM2_Supporting (Richards 2015).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024