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.

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.

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			25	3		28
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	6	8	4	19
Total	0	1	32	11	4

Variants in SETD6

This is a list of pathogenic ClinVar variants found in the SETD6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58515562-C-T		not specified	Uncertain significance (May 17, 2023)
16-58515887-G-A		not specified	Uncertain significance (Sep 13, 2023)
16-58515899-G-A		not specified	Likely benign (Feb 28, 2023)
16-58515941-C-T		not specified	Uncertain significance (Jan 20, 2023)
16-58515990-G-T		not specified	Uncertain significance (Jan 02, 2024)
16-58516004-G-C		not specified	Uncertain significance (Jun 17, 2024)
16-58516007-A-G		not specified	Uncertain significance (Dec 08, 2023)
16-58516040-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-58516046-G-C		not specified	Uncertain significance (May 29, 2024)
16-58516080-G-A		not specified	Uncertain significance (May 29, 2024)
16-58516083-G-A		not specified	Uncertain significance (May 24, 2024)
16-58516208-T-A		not specified	Uncertain significance (Apr 08, 2024)
16-58516222-C-T			Uncertain significance (Jan 01, 2019)
16-58516268-A-G		not specified	Uncertain significance (Jul 11, 2023)
16-58516276-G-A		not specified	Uncertain significance (May 03, 2023)
16-58516292-C-G		not specified	Uncertain significance (Nov 21, 2022)
16-58516482-G-A			Likely benign (Jun 01, 2024)
16-58516639-A-G		not specified	Uncertain significance (Dec 06, 2022)
16-58516641-C-T		not specified	Uncertain significance (Jul 06, 2021)
16-58516650-G-C		not specified	Uncertain significance (Oct 03, 2022)
16-58516671-A-G		not specified	Uncertain significance (Jan 24, 2024)
16-58516881-A-G		not specified	Uncertain significance (Dec 07, 2021)
16-58516902-C-T		not specified	Uncertain significance (Jan 31, 2022)
16-58518061-G-A		not specified	Uncertain significance (Jan 31, 2024)
16-58518088-A-G		not specified	Uncertain significance (Aug 16, 2021)

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