KANSL2

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

Basic information

Region (hg38): 12:48653210-48682238

Previous symbols: [ "C12orf41" ]

Links

ENSG00000139620 ∙ NCBI:54934 ∙ OMIM:615488 ∙ HGNC:26024 ∙ Uniprot:Q9H9L4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KANSL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KANSL2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in KANSL2

This is a list of pathogenic ClinVar variants found in the KANSL2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-48654142-A-C		not specified	Uncertain significance (May 27, 2022)
12-48654153-T-A		not specified	Uncertain significance (Jan 11, 2023)
12-48660451-T-A		Intellectual disability	Likely benign (Jan 01, 2019)
12-48660460-G-A		not specified	Uncertain significance (May 26, 2024)
12-48660481-T-A		not specified	Uncertain significance (Jan 20, 2023)
12-48660483-C-T		not specified	Uncertain significance (Dec 08, 2023)
12-48660604-G-A		not specified	Uncertain significance (Jun 14, 2022)
12-48667750-C-G		not specified	Uncertain significance (Mar 21, 2023)
12-48669125-G-A		not specified	Uncertain significance (May 30, 2024)
12-48669179-T-C		not specified	Uncertain significance (Dec 22, 2023)
12-48669197-C-T		not specified	Uncertain significance (Nov 13, 2023)
12-48669204-A-G		not specified	Uncertain significance (Mar 29, 2024)
12-48671823-G-A		not specified	Uncertain significance (Mar 29, 2022)
12-48671891-A-C		not specified	Uncertain significance (Jan 23, 2023)
12-48679661-T-G		not specified	Uncertain significance (Jun 01, 2023)
12-48679790-G-A		not specified	Uncertain significance (May 08, 2023)
12-48679819-G-C		not specified	Uncertain significance (Jul 08, 2022)
12-48679829-A-C		not specified	Uncertain significance (Jun 07, 2023)
12-48681449-T-C		not specified	Uncertain significance (Aug 30, 2022)
12-48681457-T-C		not specified	Uncertain significance (Mar 20, 2023)
12-48681560-G-A		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KANSL2	protein_coding	protein_coding	ENST00000420613	9	28838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.880	0.120	124784	0	4	124788	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	198	267	0.743	0.0000138	3202
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000333	0.0000333
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000889	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000165	0.000165

dbNSFP

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}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.365
• hipred: Y
• hipred_score: 0.528
• ghis: 0.539

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Kansl2

Gene ontology

• Biological process: histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K16 acetylation
• Cellular component: histone acetyltransferase complex;nucleoplasm;cytosol;plasma membrane;actin cytoskeleton;NSL complex
• Molecular function: protein binding;histone acetyltransferase activity (H4-K5 specific);histone acetyltransferase activity (H4-K8 specific);histone acetyltransferase activity (H4-K16 specific)