SETD6

SET domain containing 6, protein lysine methyltransferase, the group of SET domain containing

Basic information

Region (hg38): 16:58515479-58523842

Links

ENSG00000103037

∙ NCBI:79918 ∙ OMIM:616424 ∙ HGNC:26116 ∙ Uniprot:Q8TBK2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

colorectal cancer (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SETD6 gene.

not_specified (75 variants)
not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETD6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001160305.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			72 clinvar	4 clinvar		76
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SETD6	protein_coding	protein_coding	ENST00000219315	8	5049

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.84e-18	0.000917	125296	1	451	125748	0.00180

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.390	270	253	1.07	0.0000133	3003
Missense in Polyphen		91	79.469	1.1451		980
Synonymous	-2.11	131	104	1.26	0.00000566	946
Loss of Function	-0.744	25	21.3	1.17	9.07e-7	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00164	0.00163
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00366	0.00343
Finnish	0.000393	0.000323
European (Non-Finnish)	0.00238	0.00238
Middle Eastern	0.00366	0.00343
South Asian	0.00127	0.00121
Other	0.00408	0.00408

dbNSFP

Source: dbNSFP

Function: FUNCTION: Protein-lysine N-methyltransferase. Monomethylates 'Lys- 310' of the RELA subunit of NF-kappa-B complex, leading to down- regulate NF-kappa-B transcription factor activity (PubMed:21131967). Monomethylates 'Lys-8' of H2AZ (H2AZK8me1) (PubMed:23324626). Required for the maintenance of embryonic stem cell self-renewal (By similarity). {ECO:0000250|UniProtKB:Q9CWY3, ECO:0000269|PubMed:21131967, ECO:0000269|PubMed:23324626}.;
Pathway: Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Chromatin organization (Consensus)

Intolerance Scores

loftool: 0.737
rvis_EVS: 0.13
rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

pHI: 0.377
hipred: N
hipred_score: 0.407
ghis: 0.504

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.809

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Setd6
Phenotype: vision/eye phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype;

Gene ontology

Biological process: peptidyl-lysine monomethylation;stem cell population maintenance;negative regulation of NF-kappaB transcription factor activity;histone lysine methylation;stem cell differentiation;regulation of inflammatory response
Cellular component: nucleus;nucleoplasm;cytosol
Molecular function: protein binding;protein-lysine N-methyltransferase activity;NF-kappaB binding