rs71929101
chr10-75022147-GGAAGAAGAAGAA-Gchr10-75022147-GGAAGAAGAAGAA-GGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAAGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAAGAAGAAchr10-75022147-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAAGAAGAAGAA
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_012330.4(KAT6B):c.3301_3312del(p.Glu1101_Glu1104del) variant causes a inframe deletion change. The variant allele was found at a frequency of 0.00000125 in 1,605,904 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. E1097E) has been classified as Likely benign.
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 22)
Exomes 𝑓: 6.9e-7 ( 0 hom. )
Consequence
KAT6B
NM_012330.4 inframe_deletion
NM_012330.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.72
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 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KAT6B | NM_012330.4 | c.3301_3312del | p.Glu1101_Glu1104del | inframe_deletion | 16/18 | ENST00000287239.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KAT6B | ENST00000287239.10 | c.3301_3312del | p.Glu1101_Glu1104del | inframe_deletion | 16/18 | 1 | NM_012330.4 | P2 | |
ENST00000413431.1 | n.65+2951_65+2962del | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000667 AC: 1AN: 150036Hom.: 0 Cov.: 22
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GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1455868Hom.: 0 AF XY: 0.00000138 AC XY: 1AN XY: 724470
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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 | Apr 16, 2022 | 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant, c.3301_3312del, results in the deletion of 4 amino acid(s) of the KAT6B protein (p.Glu1101_Glu1104del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KAT6B-related conditions. - |
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at