8-41933987-CTCTTT-C
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_006766.5(KAT6A):c.4228_4232delAAAGA(p.Lys1410GlyfsTer7) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Consequence
NM_006766.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Autosomal dominant intellectual disability-craniofacial anomalies-cardiac defects syndrome Pathogenic:2
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Inborn genetic diseases Pathogenic:1
The c.4228_4232delAAAGA pathogenic mutation (also known as p.K1410GFS*7), located in coding exon 16 of the KAT6A gene, results from a deletion of 5 nucleotides at nucleotide positions 4228 to 4232, causing a translational frameshift with a predicted alternate stop codon. This mutation is located downstream of the nonsense-mediated mRNA decay (NMD) boundary. Typically, mRNA transcripts from alterations located downstream of NMD boundaries will not be degraded, resulting in translation of a truncated protein. A de novo protein truncating variant (c.4292dupT), located downstream of the c.4228_4232delAAAGA pathogenic mutation, has been reported in an individual presenting with global developmental delay, significant hypotonia, cardiac defects and dysmorphic features (Tham E et al. Am J Hum Genet. 2015; 96(3):507-13). Therefore, both alterations likely escape NMD and are expected to result in loss of function by premature protein truncation. As such, the c.4228_4232delAAAGA alteration is interpreted as a disease-causing mutation -
See cases Pathogenic:1
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not provided Pathogenic:1
Identified in a patient with intellectual disability and speech delay in the published literature (Kennedy et al., 2019); Frameshift variant predicted to result in protein truncation, as the last 595 amino acids are replaced with 6 different amino acids; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30245513) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at