KANSL2

protein-coding

KAT8 regulatory NSL complex subunit 2, the group of NSL histone acetyltransferase complex|Small nucleolar RNA protein coding host genes|MicroRNA protein coding host genes

Gene summary

Predicted to be involved in positive regulation of DNA-templated transcription. Located in cytosol; nucleoplasm; and plasma membrane. Part of histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C12orf41

MANE transcript

NM_017822.4

Inheritance

—

ClinVar variants

U:49B:1

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr12:48,653,211-48,682,238

External References & Databases

Ensembl (ENSG00000139620)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 kb

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GenCC 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 KANSL2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 1

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017822.4. 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			2 clinvar			2
missense			44 clinvar	1 clinvar		45
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	49	1	0	50

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017822.4	RefSeq	NP_060292.3	9	MANE Select
ENST00000420613.7	Ensembl	ENSP00000415436.3	9	MANE Select
ENST00000546701.5	Ensembl	ENSP00000448131.1	3	Standard
ENST00000547087.5	Ensembl	ENSP00000447608.1	5	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

protein binding
histone acetyltransferase activity (H4-K5 specific)
histone acetyltransferase activity (H4-K8 specific)
histone acetyltransferase activity (H4-K16 specific)

Cellular Component

histone acetyltransferase complex
nucleoplasm
cytosol
plasma membrane
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000420613
Coding exons: 9
Length: 28838
Individuals with no LoFs: 124784
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 124788
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.49	198	267	0.743	0.0000138	3202
Missense (PolyPhen)		37	66.444	0.55686		843
Synonymous	0.271	91	94.3	0.965	0.00000453	957
Loss of Function	3.84	4	24.5	0.163	0.00000162	269

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000033	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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: 0.110

Intolerance Scores

RVIS EVS: 0.15
RVIS percentile EVS: 64.51

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