SETMAR
SET domain and mariner transposase fusion gene, the group of DNA transposon derived genes|SET domain containing
Basic information
Region (hg38): 3:4303332-4317265
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (61 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETMAR gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006515.4. 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 | 3 | |||||
| missense | 58 | 61 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 6 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SETMAR | protein_coding | protein_coding | ENST00000358065 | 3 | 14264 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000102 | 0.821 | 125629 | 2 | 95 | 125726 | 0.000386 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.263 | 362 | 376 | 0.962 | 0.0000208 | 4463 |
| Missense in Polyphen | 71 | 65.409 | 1.0855 | 831 | ||
| Synonymous | 0.206 | 137 | 140 | 0.978 | 0.00000813 | 1296 |
| Loss of Function | 1.24 | 8 | 12.8 | 0.626 | 7.61e-7 | 175 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000799 | 0.000797 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000598 | 0.000598 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000273 | 0.000273 |
| Middle Eastern | 0.000598 | 0.000598 |
| South Asian | 0.00131 | 0.00124 |
| Other | 0.000491 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Protein derived from the fusion of a methylase with the transposase of an Hsmar1 transposon that plays a role in DNA double-strand break repair, stalled replication fork restart and DNA integration. DNA-binding protein, it is indirectly recruited to sites of DNA damage through protein-protein interactions. Has also kept a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity (PubMed:16332963, PubMed:16672366, PubMed:17877369, PubMed:17403897, PubMed:18263876, PubMed:22231448, PubMed:24573677, PubMed:20521842). In parallel, has a histone methyltransferase activity and methylates 'Lys-4' and 'Lys-36' of histone H3. Specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining (PubMed:16332963, PubMed:21187428, PubMed:22231448). Also regulates replication fork processing, promoting replication fork restart and regulating DNA decatenation through stimulation of the topoisomerase activity of TOP2A (PubMed:18790802, PubMed:20457750). {ECO:0000269|PubMed:16332963, ECO:0000269|PubMed:16672366, ECO:0000269|PubMed:17403897, ECO:0000269|PubMed:17877369, ECO:0000269|PubMed:18790802, ECO:0000269|PubMed:20457750, ECO:0000269|PubMed:20521842, ECO:0000269|PubMed:21187428, ECO:0000269|PubMed:22231448, ECO:0000269|PubMed:24573677, ECO:0000303|PubMed:18263876}.;
- Pathway
- Lysine degradation - Homo sapiens (human);Histone Modifications
(Consensus)
Recessive Scores
- pRec
- 0.0930
Intolerance Scores
- loftool
- 0.318
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.6
Haploinsufficiency Scores
- pHI
- 0.0744
- hipred
- Y
- hipred_score
- 0.551
- ghis
- 0.427
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Setmar
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- DNA double-strand break processing;DNA catabolic process, endonucleolytic;double-strand break repair via nonhomologous end joining;cell population proliferation;histone H3-K36 methylation;DNA integration;replication fork processing;mitotic DNA integrity checkpoint;histone H3-K4 methylation;negative regulation of cell cycle arrest;nucleic acid phosphodiester bond hydrolysis;histone H3-K36 dimethylation;positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity;positive regulation of double-strand break repair via nonhomologous end joining;negative regulation of chromosome organization
- Cellular component
- condensed chromosome;nucleus;nucleolus;site of double-strand break
- Molecular function
- single-stranded DNA endodeoxyribonuclease activity;DNA binding;double-stranded DNA binding;single-stranded DNA binding;endonuclease activity;protein binding;zinc ion binding;histone methyltransferase activity (H3-K4 specific);protein homodimerization activity;DNA topoisomerase binding;histone methyltransferase activity (H3-K36 specific)