10-74842943-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BS1_Supporting
The NM_012330.4(KAT6B):c.86A>T(p.Glu29Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,614,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000032 ( 0 hom. )
Consequence
KAT6B
NM_012330.4 missense
NM_012330.4 missense
Scores
5
5
2
Clinical Significance
Conservation
PhyloP100: 8.95
Genes affected
KAT6B (HGNC:17582): (lysine acetyltransferase 6B) The protein encoded by this gene is a histone acetyltransferase and component of the MOZ/MORF protein complex. In addition to its acetyltransferase activity, the encoded protein has transcriptional activation activity in its N-terminal end and transcriptional repression activity in its C-terminal end. This protein is necessary for RUNX2-dependent transcriptional activation and could be involved in brain development. Mutations have been found in patients with genitopatellar syndrome. A translocation of this gene and the CREBBP gene results in acute myeloid leukemias. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, KAT6B
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000197 (3/152214) while in subpopulation NFE AF= 0.0000441 (3/68028). AF 95% confidence interval is 0.0000117. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6B | NM_012330.4 | c.86A>T | p.Glu29Val | missense_variant | 3/18 | ENST00000287239.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6B | ENST00000287239.10 | c.86A>T | p.Glu29Val | missense_variant | 3/18 | 1 | NM_012330.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152214Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251462Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
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GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727242
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Genitopatellar syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 04, 2022 | This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 29 of the KAT6B protein (p.Glu29Val). This variant is present in population databases (no rsID available, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1363581). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
Polyphen
1.0, 1.0
.;D;.;D;D;D;.;.;.;.;.;D;.;D;.;D;D;.;.;.;.;.;.;D;.
Vest4
0.69, 0.67, 0.65, 0.70, 0.70
MutPred
Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);Loss of disorder (P = 0.0118);
MVP
0.73
MPC
1.2
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at