KANSL3

KAT8 regulatory NSL complex subunit 3, the group of NSL histone acetyltransferase complex

Basic information

Region (hg38): 2:96593169-96642787

Previous symbols: [ "KIAA1310" ]

Links

ENSG00000114982 ∙ NCBI:55683 ∙ OMIM:617742 ∙ HGNC:25473 ∙ Uniprot:Q9P2N6 ∙ 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 KANSL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KANSL3 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in KANSL3

This is a list of pathogenic ClinVar variants found in the KANSL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96595630-C-T		not specified	Uncertain significance (May 30, 2023)
2-96601689-G-A		not specified	Uncertain significance (Dec 14, 2021)
2-96601720-T-A		not specified	Uncertain significance (Feb 07, 2023)
2-96602224-T-C		not specified	Uncertain significance (Jun 10, 2022)
2-96602304-C-T		not specified	Uncertain significance (May 08, 2023)
2-96602796-G-A		not specified	Uncertain significance (Feb 06, 2023)
2-96604271-A-C			Likely benign (Sep 01, 2023)
2-96604276-G-A		not specified	Uncertain significance (Nov 09, 2022)
2-96604285-C-T		not specified	Uncertain significance (May 24, 2023)
2-96604334-C-A		not specified	Uncertain significance (Jun 03, 2024)
2-96604369-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-96604815-C-A		not specified	Uncertain significance (Nov 29, 2021)
2-96605329-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-96605344-G-C		not specified	Uncertain significance (Jun 06, 2023)
2-96605380-T-C		not specified	Uncertain significance (Apr 19, 2024)
2-96605403-C-A		not specified	Uncertain significance (Dec 28, 2022)
2-96605415-T-G		not specified	Uncertain significance (Dec 06, 2021)
2-96605442-T-C		not specified	Uncertain significance (May 28, 2023)
2-96605471-C-A		not specified	Uncertain significance (Jun 02, 2023)
2-96605473-C-T		not specified	Uncertain significance (Dec 15, 2023)
2-96608531-A-G		not specified	Uncertain significance (Sep 06, 2022)
2-96608621-G-A		not specified	Uncertain significance (Nov 17, 2023)
2-96608899-C-G		not specified	Uncertain significance (Dec 12, 2023)
2-96608952-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-96608953-G-A		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KANSL3	protein_coding	protein_coding	ENST00000431828	20	49618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000198	124627	0	3	124630	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	335	489	0.686	0.0000265	5592
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.00000891	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.104

Intolerance Scores

• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.58

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.591
• ghis: 0.520

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: Kansl3

Gene ontology

• Biological process: histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K16 acetylation
• Cellular component: histone acetyltransferase complex;nucleus;nucleoplasm;nucleolus;intracellular membrane-bounded organelle;NSL complex
• Molecular function: histone acetyltransferase activity (H4-K5 specific);histone acetyltransferase activity (H4-K8 specific);histone acetyltransferase activity (H4-K16 specific)