SETD6
Basic information
Region (hg38): 16:58515479-58523842
Links
Phenotypes
GenCC
Source:
- colorectal cancer (Limited), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | |||||
missense | 72 | 76 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 73 | 5 | 0 |
GnomAD
Source:
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:
- 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