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NM_012330.4(KAT6B):c.3987_3988del (p.Ala1331fs) AND Genitopatellar syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 26, 2020
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:
RCV001382519.7

Allele description [Variation Report for NM_012330.4(KAT6B):c.3987_3988del (p.Ala1331fs)]

NM_012330.4(KAT6B):c.3987_3988del (p.Ala1331fs)

Gene:
KAT6B:lysine acetyltransferase 6B [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q22.2
Genomic location:
Preferred name:
NM_012330.4(KAT6B):c.3987_3988del (p.Ala1331fs)
HGVS:
  • NC_000010.11:g.75028811_75028812del
  • NG_032048.1:g.207399_207400del
  • NM_001256468.2:c.3438_3439del
  • NM_001256469.2:c.3111_3112del
  • NM_001370132.1:c.2949_2950del
  • NM_001370133.1:c.2298_2299del
  • NM_001370134.1:c.1902_1903del
  • NM_001370135.1:c.1644_1645del
  • NM_001370136.1:c.3987_3988del
  • NM_001370137.1:c.3987_3988del
  • NM_001370138.1:c.3438_3439del
  • NM_001370139.1:c.3111_3112del
  • NM_001370140.1:c.3111_3112del
  • NM_001370141.1:c.3111_3112del
  • NM_001370142.1:c.3111_3112del
  • NM_001370143.1:c.2922_2923del
  • NM_001370144.1:c.2922_2923del
  • NM_012330.4:c.3987_3988delMANE SELECT
  • NP_001243397.1:p.Ala1148fs
  • NP_001243398.1:p.Ala1039fs
  • NP_001357061.1:p.Ala985fs
  • NP_001357062.1:p.Ala768fs
  • NP_001357063.1:p.Ala636fs
  • NP_001357064.1:p.Ala550fs
  • NP_001357065.1:p.Ala1331fs
  • NP_001357066.1:p.Ala1331fs
  • NP_001357067.1:p.Ala1148fs
  • NP_001357068.1:p.Ala1039fs
  • NP_001357069.1:p.Ala1039fs
  • NP_001357070.1:p.Ala1039fs
  • NP_001357071.1:p.Ala1039fs
  • NP_001357072.1:p.Ala976fs
  • NP_001357073.1:p.Ala976fs
  • NP_036462.2:p.Ala1331fs
  • NC_000010.10:g.76788569_76788570del
  • NC_000010.10:g.76788569_76788570delAT
Protein change:
A1039fs
Links:
dbSNP: rs2134235713
NCBI 1000 Genomes Browser:
rs2134235713
Molecular consequence:
  • NM_001256468.2:c.3438_3439del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001256469.2:c.3111_3112del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370132.1:c.2949_2950del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370133.1:c.2298_2299del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370134.1:c.1902_1903del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370135.1:c.1644_1645del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370136.1:c.3987_3988del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370137.1:c.3987_3988del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370138.1:c.3438_3439del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370139.1:c.3111_3112del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370140.1:c.3111_3112del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370141.1:c.3111_3112del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370142.1:c.3111_3112del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370143.1:c.2922_2923del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001370144.1:c.2922_2923del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012330.4:c.3987_3988del - 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
SCV001581342Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Apr 26, 2020) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Whole-exome-sequencing identifies mutations in histone acetyltransferase gene KAT6B in individuals with the Say-Barber-Biesecker variant of Ohdo syndrome.

Clayton-Smith J, O'Sullivan J, Daly S, Bhaskar S, Day R, Anderson B, Voss AK, Thomas T, Biesecker LG, Smith P, Fryer A, Chandler KE, Kerr B, Tassabehji M, Lynch SA, Krajewska-Walasek M, McKee S, Smith J, Sweeney E, Mansour S, Mohammed S, Donnai D, et al.

Am J Hum Genet. 2011 Nov 11;89(5):675-81. doi: 10.1016/j.ajhg.2011.10.008.

PubMed [citation]
PMID:
22077973
PMCID:
PMC3213399

Further delineation of the KAT6B molecular and phenotypic spectrum.

Gannon T, Perveen R, Schlecht H, Ramsden S, Anderson B, Kerr B, Day R, Banka S, Suri M, Berland S, Gabbett M, Ma A, Lyonnet S, Cormier-Daire V, Yilmaz R, Borck G, Wieczorek D, Anderlid BM, Smithson S, Vogt J, Moore-Barton H, Simsek-Kiper PO, et al.

Eur J Hum Genet. 2015 Sep;23(9):1165-70. doi: 10.1038/ejhg.2014.248. Epub 2014 Nov 26.

PubMed [citation]
PMID:
25424711
PMCID:
PMC4351891
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001581342.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the KAT6B protein. Other variant(s) that disrupt this region (p.Ser1402Cysfs*5) have been determined to be pathogenic (PMID: 22077973, 25424711, 28696035). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has not been reported in the literature in individuals with KAT6B-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the KAT6B gene (p.Ala1331Profs*10). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 743 amino acids of the KAT6B protein.

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

Last Updated: Sep 29, 2024