KANSL1L

protein-coding

KAT8 regulatory NSL complex subunit 1 like

Gene summary

Predicted to enable histone acetyltransferase binding activity. Predicted to be part of NSL complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C2orf67

MANE transcript

NM_152519.4

Inheritance

—

ClinVar variants

U:134B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr2:210,021,421-210,171,409

External References & Databases

Ensembl (ENSG00000144445)

Transcript & Mutation Effects

hg38 • Region Span ~150.0 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 KANSL1L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152519.4. 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				1 clinvar	1 clinvar	2
missense			132 clinvar	4 clinvar	1 clinvar	137
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	134	5	2	141

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152519.4	RefSeq	NP_689732.2	14	MANE Select
ENST00000281772.14	Ensembl	ENSP00000281772.8	14	MANE Select
NM_001307976.2	RefSeq	NP_001294905.1	13	Standard
ENST00000415553.1	Ensembl	ENSP00000388182.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

histone H4-K5 acetylation
histone H4-K8 acetylation
histone H4-K16 acetylation

Molecular Function

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

Cellular Component

NSL complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000281772
Coding exons: 14
Length: 149961
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 125748
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.245	470	485	0.969	0.0000228	6502
Missense (PolyPhen)		134	156.33	0.85718		2094
Synonymous	-1.15	196	177	1.11	0.00000844	1801
Loss of Function	5.25	11	51.8	0.212	0.00000288	630

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00044	0.00044	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000065	0.000065	rare
Other	0.00033	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.25
RVIS percentile EVS: 69.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
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