Gene Gene information from NCBI Gene database.
Entrez ID 29072
Gene name SET domain containing 2, histone lysine methyltransferase
Gene symbol SETD2
Synonyms (NCBI Gene)
HBP231HIF-1HIP-1HSPC069HYPBKMT3ALLSMRD70RAPASSET2p231HBP
Chromosome 3
Chromosome location 3p21.31
Summary Huntington`s disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting
SNPs SNP information provided by dbSNP.
16
SNP ID Visualize variation Clinical significance Consequence
rs115788094 G>A,T Conflicting-interpretations-of-pathogenicity, not-provided Non coding transcript variant, missense variant, coding sequence variant
rs869025569 T>- Pathogenic Frameshift variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs869025570 A>C Pathogenic Genic downstream transcript variant, missense variant, non coding transcript variant, coding sequence variant
rs869025571 G>A Pathogenic Stop gained, non coding transcript variant, coding sequence variant
rs869025572 A>- Pathogenic Frameshift variant, non coding transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
153
miRTarBase ID miRNA Experiments Reference
MIRT050126 hsa-miR-26a-5p CLASH 23622248
MIRT044337 hsa-miR-106b-5p CLASH 23622248
MIRT053100 hsa-miR-199b-5p Luciferase reporter assayqRT-PCRWestern blot 23594994
MIRT437893 hsa-miR-21-5p ChIP-seqLuciferase reporter assay 24983504
MIRT731626 hsa-miR-186-5p Luciferase reporter assay 27159677
Transcription factors Transcription factors information provided by TRRUST V2 database.
2
Transcription factor Regulation Reference
HIF1A Activation 18842833
HIF1A Unknown 19091749
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
54
GO ID Ontology Definition Evidence Reference
GO:0000045 Process Autophagosome assembly IDA 28890335
GO:0002376 Process Immune system process IEA
GO:0005515 Function Protein binding IPI 17500595, 19141475, 21988832, 28753426, 36537238
GO:0005634 Component Nucleus IBA
GO:0005634 Component Nucleus IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
612778 18420 ENSG00000181555
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9BYW2
Protein name Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.359) (HIF-1) (Huntingtin yeast partner B) (Huntingtin-interacting protein 1) (HIP-1) (Huntingtin-interacting protein B) (Lysine N-methyltransferase 3A) (Protein-lysine N-methyltransferase SETD2) (EC 2.1.1
Protein function Histone methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using dimethylated 'Lys-36' (H3K36me2) as substrate (PubMed:16118227, PubMed:19141475, PubMed:21526191, PubMed:21792193, PubMed:23043551, PubMed:27474439
PDB 2A7O , 2MDC , 2MDI , 2MDJ , 4FMU , 4H12 , 5JJY , 5JLB , 5JLE , 5LSS , 5LSX , 5LSY , 5LSZ , 5LT6 , 5LT7 , 5LT8 , 5V21 , 5V22 , 6J9J , 6VDB , 7EA8 , 7EVR , 7EVS , 7LZB , 7LZD , 7LZF , 7TY2 , 7TY3 , 8Q5P , 8RZU , 9EGZ , 9EH0 , 9EH1 , 9EH2
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF17907 AWS 1511 1547 AWS domain Domain
PF00856 SET 1561 1667 SET domain Family
PF00397 WW 2391 2420 WW domain Domain
PF08236 SRI 2467 2557 SRI (Set2 Rpb1 interacting) domain Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:11461154}.
Sequence
MKQLQPQPPPKMGDFYDPEHPTPEEEENEAKIENVQKTGFIKGPMFKGVASSRFLPKGTK
TKVNLEEQGRQKVSFSFSLTKKTLQNRFLTALGNEKQSDTPNPPAVPLQVDSTPKMKMEI
GDTLSTAEESSPPKSRVELGKIHFKKHLLHVTSRPLLATTTAVASPPTHAAPLPAVIAES
TTVDSPPSSPPPPPPPAQATTLSSPAPVTEPVALPHTPITVLMAAPVPLPVDVAVRSLKE
PPIIIVPESLEADTKQDTISNSLEEHVTQILNEQADISSKKEDSHIGKDEEIPDSSKISL
SCKKTGSKKKSSQSEGIFLGSESDEDSVRTSSSQRSHDLKFSASIEKERDFKKSSAPLKS
EDLGKPSRSKTDRDDKYFSYSKLERDTRYVSSRCRSERERRRSRSHSRSERGSRTNLSYS
RSERSHYYDSDRRYHRSSPYRERTRYSRPYTDNRARESSDSEEEYKKTYSRRTSSHSSSY
RDLRTSSYSKSDRDCKTETSYLEMERRGKYSSKLERESKRTSENEAIKRCCSPPNELGFR
RGSSYSKHDSSASRYKSTLSKPIPKSDKFKNSFCCTELNEEIKQSHSFSLQTPCSKGSEL
RMINKNPEREKAGSPAPSNRLNDSPTLKKLDELPIFKSEFITHDSHDSIKELDSLSKVKN
DQLRSFCPIELNINGSPGAESDLATFCTSKTDAVLMTSDDSVTGSELSPLVKACMLSSNG
FQNISRCKEKDLDDTCMLHKKSESPFRETEPLVSPHQDKLMSMPVMTVDYSKTVVKEPVD
TRVSCCKTKDSDIYCTLNDSNPSLCNSEAENIEPSVMKISSNSFMNVHLESKPVICDSRN
LTDHSKFACEEYKQSIGSTSSASVNHFDDLYQPIGSSGIASSLQSLPPGIKVDSLTLLKC
GENTSPVLDAVLKSKKSSEFLKHAGKETIVEVGSDLPDSGKGFASRENRRNNGLSGKCLQ
EAQEEGNSILPERRGRPEISLDERGEGGHVHTSDDSEVVFSSCDLNLTMEDSDGVTYALK
CDSSGHAPEIVSTVHEDYSGSSESSNDESDSEDTDSDDSSIPRNRLQSVVVVPKNSTLPM
EETSPCSSRSSQSYRHYSDHWEDERLESRRHLYEEKFESIASKACPQTDKFFLHKGTEKN
PEISFTQSSRKQIDNRLPELSHPQSDGVDSTSHTDVKSDPLGHPNSEETVKAKIPSRQQE
ELPIYSSDFEDVPNKSWQQTTFQNRPDSRLGKTELSFSSSCEIPHVDGLHSSEELRNLGW
DFSQEKPSTTYQQPDSSYGACGGHKYQQNAEQYGGTRDYWQGNGYWDPRSGRPPGTGVVY
DRTQGQVPDSLTDDREEEENWDQQDGSHFSDQSDKFLLSLQKDKGSVQAPEISSNSIKDT
LAVNEKKDFSKNLEKNDIKDRGPLKKRRQEIESDSESDGELQDRKKVRVEVEQGETSVPP
GSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCE
CTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKK
GWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQK
GNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQ
FQRYGKEAQKCFC
GSANCRGYLGGENRVSIRAAGGKMKKERSRKKDSVDGELEALMENGEGLSDKNQVLSLSR
LMVRIETLEQKLTCLELIQNTHSQSCLKSFLERHGLSLLWIWMAELGDGRESNQKLQEEI
IKTLEHLPIPTKNMLEESKVLPIIQRWSQTKTAVPPLSEGDGYSSENTSRAHTPLNTPDP
STKLSTEADTDTPKKLMFRRLKIISENSMDSAISDATSELEGKDGKEDLDQLENVPVEEE
EELQSQQLLPQQLPECKVDSETNIEASKLPTSEPEADAEIEPKESNGTKLEEPINEETPS
QDEEEGVSDVESERSQEQPDKTVDISDLATKLLDSWKDLKEVYRIPKKSQTEKENTTTER
GRDAVGFRDQTPAPKTPNRSRERDPDKQTQNKEKRKRRSSLSPPSSAYERGTKRPDDRYD
TPTSKKKVRIKDRNKLSTEERRKLFEQEVAQREAQKQQQQMQNLGMTSPLPYDSLGYNAP
HHPFAGYPPGYPMQAYVDPSNPNAGKVLLPTPSMDPVCSPAPYDHAQPLVGHSTEPLSAP
PPVPVVPHVAAPVEVSSSQYVAQSDGVVHQDSSVAVLPVPAPGPVQGQNYSVWDSNQQSV
SVQQQYSPAQSQATIYYQGQTCPTVYGVTSPYSQTTPPIVQSYAQPSLQYIQGQQIFTAH
PQGVVVQPAAAVTTIVAPGQPQPLQPSEMVVTNNLLDLPPPSPPKPKTIVLPPNWKTARD
PEGKIYYYHVITRQTQWDPP
TWESPGDDASLEHEAEMDLGTPTYDENPMKASKKPKTAEA
DTSSELAKKSKEVFRKEMSQFIVQCLNPYRKPDCKVGRITTTEDFKHLARKLTHGVMNKE
LKYCKNPEDLECNENVKHKTKEYIKKYMQKFGAVYKP
KEDTELE
Sequence length 2564
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Lysine degradation
Metabolic pathways
  PKMTs methylate histone lysines
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
48
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Acute megakaryoblastic leukemia without down syndrome Likely pathogenic rs2043042281, rs1293916143 RCV001293748
RCV001293749
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autism spectrum disorder Likely pathogenic rs774671060 RCV003127362
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebellar vermis hypoplasia Likely pathogenic; Pathogenic rs1057523157 RCV000779643
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital cerebellar hypoplasia Likely pathogenic; Pathogenic rs1057523157 RCV001258009
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autism Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISTIC DISORDER Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
ABLEPHARON-MACROSTOMIA SYNDROME Ablepharon macrostomia syndrome BEFREE 21242666, 29927953, 30278484
★☆☆☆☆
Found in Text Mining only
Accessory kidney Accessory Kidney HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 24509477, 30967619
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 24662245
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 18026974, 30377207
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 19735869, 26595459, 26646321, 27687306, 28202515, 31155235, 31599770
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 23857671
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of rectum Adenocarcinoma Of Rectum BEFREE 20117921
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma, Clear Cell Adenocarcinoma BEFREE 21248752
★☆☆☆☆
Found in Text Mining only
Adenoid Cystic Carcinoma Adenocarcinoma CTD_human_DG 23685749
★☆☆☆☆
Found in Text Mining only