SETD6

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

Basic information

Region (hg38): 16:58515479-58523842

Links

ENSG00000103037NCBI:79918OMIM:616424HGNC:26116Uniprot:Q8TBK2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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.

EffectPLPVUSLBBSum
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

GeneTypeBio TypeTranscript Coding Exons Length
SETD6protein_codingprotein_codingENST00000219315 85049
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.84e-180.00091712529614511257480.00180
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.3902702531.070.00001333003
Missense in Polyphen9179.4691.1451980
Synonymous-2.111311041.260.00000566946
Loss of Function-0.7442521.31.179.07e-7246

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001640.00163
Ashkenazi Jewish0.00009920.0000992
East Asian0.003660.00343
Finnish0.0003930.000323
European (Non-Finnish)0.002380.00238
Middle Eastern0.003660.00343
South Asian0.001270.00121
Other0.004080.00408

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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