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GeneBe

SETMAR

SET domain and mariner transposase fusion gene, the group of DNA transposon derived genes|SET domain containing

Basic information

Region (hg38): 3:4303331-4317265

Links

ENSG00000170364NCBI:6419OMIM:609834HGNC:10762Uniprot:Q53H47AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (23 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.

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
3
clinvar
3
missense
22
clinvar
1
clinvar
23
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 22 4 0

Variants in SETMAR

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

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

Position Type Phenotype Significance ClinVar
3-4303393-C-G not specified Uncertain significance (Apr 03, 2023)2532231
3-4303398-C-T not specified Uncertain significance (Sep 22, 2022)2405805
3-4303413-G-A not specified Uncertain significance (Feb 27, 2024)2348386
3-4303437-G-A not specified Uncertain significance (Jun 22, 2023)2605275
3-4303485-G-A not specified Uncertain significance (Mar 01, 2024)3160707
3-4303486-T-G not specified Uncertain significance (Sep 10, 2021)2358953
3-4303494-T-G not specified Uncertain significance (Sep 10, 2021)3160708
3-4303521-T-G not specified Uncertain significance (Dec 03, 2021)2230214
3-4312933-C-G not specified Uncertain significance (Oct 04, 2022)2316333
3-4312961-G-A not specified Uncertain significance (Jan 24, 2024)3160709
3-4312980-C-T not specified Uncertain significance (Jun 29, 2023)2608522
3-4313174-A-G not specified Uncertain significance (Nov 17, 2022)2204532
3-4313201-C-T not specified Uncertain significance (Aug 17, 2022)2401031
3-4313220-C-T not specified Uncertain significance (Jul 20, 2021)2238235
3-4313238-G-C not specified Uncertain significance (Aug 28, 2023)2621831
3-4313274-T-C not specified Uncertain significance (Nov 16, 2021)2383894
3-4313448-G-A not specified Uncertain significance (Apr 26, 2023)2524808
3-4313483-G-A not specified Uncertain significance (Jan 05, 2022)2270482
3-4313504-G-A not specified Uncertain significance (Apr 17, 2023)2536843
3-4313580-A-T not specified Uncertain significance (Feb 21, 2024)2376612
3-4313581-T-C Likely benign (Sep 01, 2022)2653449
3-4313583-G-A not specified Uncertain significance (Dec 07, 2021)2265458
3-4313640-T-A not specified Likely benign (Nov 07, 2022)2403619
3-4313663-G-A not specified Uncertain significance (Oct 26, 2022)2304213
3-4313708-A-C not specified Uncertain significance (Nov 21, 2022)2328643

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SETMARprotein_codingprotein_codingENST00000358065 314264
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001020.8211256292951257260.000386
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2633623760.9620.00002084463
Missense in Polyphen7165.4091.0855831
Synonymous0.2061371400.9780.000008131296
Loss of Function1.24812.80.6267.61e-7175

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007990.000797
Ashkenazi Jewish0.000.00
East Asian0.0005980.000598
Finnish0.000.00
European (Non-Finnish)0.0002730.000273
Middle Eastern0.0005980.000598
South Asian0.001310.00124
Other0.0004910.000489

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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)