KANSL3
protein-codingKAT8 regulatory NSL complex subunit 3, the group of NSL histone acetyltransferase complex
Gene summary
Involved in regulation of mitochondrial transcription. Located in mitochondrion and nucleoplasm. Part of NSL complex. [provided by Alliance of Genome Resources, Jul 2025]
- KIAA1310
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KANSL3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001115016.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 107 | 2 | 109 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 113 | 2 | 0 | 115 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001108488.1 | 20 | MANE Select | |
| Ensembl | ENSP00000396749.1 | 20 | MANE Select | |
| RefSeq | NP_001336185.1 | 21 | Standard | |
| RefSeq | NP_001336186.1 | 21 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Chromatin modifying enzymes
- HATs acetylate histones
- Chromatin organization
Biological Process
- histone H4-K5 acetylation
- histone H4-K8 acetylation
- histone H4-K16 acetylation
Molecular Function
- histone acetyltransferase activity (H4-K5 specific)
- histone acetyltransferase activity (H4-K8 specific)
- histone acetyltransferase activity (H4-K16 specific)
Cellular Component
- histone acetyltransferase complex
- nucleus
- nucleoplasm
- nucleolus
- intracellular membrane-bounded organelle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000431828
- Coding exons
- 20
- Length
- 49618
- Individuals with no LoFs
- 124627
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 124630
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.47 | 335 | 489 | 0.686 | 0.0000265 | 5592 |
| Missense (PolyPhen) | 113 | 187.05 | 0.60413 | 2061 | ||
| Synonymous | 2.21 | 144 | 182 | 0.791 | 0.00000919 | 1876 |
| Loss of Function | 5.52 | 2 | 39.3 | 0.0509 | 0.00000204 | 460 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.0000089 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: As part of the NSL complex it is involved in acetylation of nucleosomal histone H4 on several lysine residues and therefore may be involved in the regulation of transcription. {ECO:0000269|PubMed:20018852}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- RVIS EVS
- 0.27
- RVIS percentile EVS
- 70.58
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |