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

ENSG00000170364 ∙ NCBI:6419 ∙ OMIM:609834 ∙ HGNC:10762 ∙ Uniprot:Q53H47 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		3
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	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)
3-4303398-C-T		not specified	Uncertain significance (Sep 22, 2022)
3-4303413-G-A		not specified	Uncertain significance (Feb 27, 2024)
3-4303437-G-A		not specified	Uncertain significance (Jun 22, 2023)
3-4303485-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-4303486-T-G		not specified	Uncertain significance (Sep 10, 2021)
3-4303494-T-G		not specified	Uncertain significance (Sep 10, 2021)
3-4303521-T-G		not specified	Uncertain significance (Dec 03, 2021)
3-4312933-C-G		not specified	Uncertain significance (Oct 04, 2022)
3-4312961-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-4312980-C-T		not specified	Uncertain significance (Jun 29, 2023)
3-4313174-A-G		not specified	Uncertain significance (Nov 17, 2022)
3-4313201-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-4313220-C-T		not specified	Uncertain significance (Jul 20, 2021)
3-4313238-G-C		not specified	Uncertain significance (Aug 28, 2023)
3-4313274-T-C		not specified	Uncertain significance (Nov 16, 2021)
3-4313448-G-A		not specified	Uncertain significance (Apr 26, 2023)
3-4313483-G-A		not specified	Uncertain significance (Jan 05, 2022)
3-4313504-G-A		not specified	Uncertain significance (Apr 17, 2023)
3-4313580-A-T		not specified	Uncertain significance (Feb 21, 2024)
3-4313581-T-C			Likely benign (Sep 01, 2022)
3-4313583-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-4313640-T-A		not specified	Likely benign (Nov 07, 2022)
3-4313663-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-4313708-A-C		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

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: 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

	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)