Gene Gene information from NCBI Gene database.
Entrez ID 23067
Gene name SET domain containing 1B, histone lysine methyltransferase
Gene symbol SETD1B
Synonyms (NCBI Gene)
IDDSELDKMT2GSet1B
Chromosome 12
Chromosome location 12q24.31
Summary SET1B is a component of a histone methyltransferase complex that produces trimethylated histone H3 at Lys4 (Lee et al., 2007 [PubMed 17355966]).[supplied by OMIM, Mar 2008]
SNPs SNP information provided by dbSNP.
2
SNP ID Visualize variation Clinical significance Consequence
rs1592977444 AG>- Likely-pathogenic Coding sequence variant, frameshift variant
rs1592988488 ->C Pathogenic Coding sequence variant, frameshift variant
miRNA miRNA information provided by mirtarbase database.
1013
miRTarBase ID miRNA Experiments Reference
MIRT019516 hsa-miR-151a-5p Sequencing 20371350
MIRT025865 hsa-miR-7-5p Sequencing 20371350
MIRT027194 hsa-miR-103a-3p Sequencing 20371350
MIRT028695 hsa-miR-27a-3p Sequencing 20371350
MIRT031924 hsa-miR-16-5p Sequencing 20371350
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
27
GO ID Ontology Definition Evidence Reference
GO:0003676 Function Nucleic acid binding IEA
GO:0003723 Function RNA binding IEA
GO:0005515 Function Protein binding IPI 17998332, 22266653, 22665483, 26886794, 37030068
GO:0005634 Component Nucleus IDA 38003223
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
611055 29187 ENSG00000139718
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9UPS6
Protein name Histone-lysine N-methyltransferase SETD1B (EC 2.1.1.364) (Lysine N-methyltransferase 2G) (SET domain-containing protein 1B) (hSET1B)
Protein function Histone methyltransferase that catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism (PubMed:17355966, PubMed:25561738). Part of chromatin remodelin
PDB 3UVO , 4ES0 , 8ILZ , 8WXV
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00076 RRM_1 108 175 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) Domain
PF11764 N-SET 1679 1821 COMPASS (Complex proteins associated with Set1p) component N Domain
PF00856 SET 1838 1944 SET domain Family
Sequence
MENSHPPHHHHQQPPPQPGPSGERRNHHWRSYKLMIDPALKKGHHKLYRYDGQHFSLAMS
SNRPVEIVEDPRVVGIWTKNKELELSVPKFKIDEFYVGPVPPKQVTFAKLNDNIRENFLR
DMCKKYGEVEEVEILYNPKTKKHLGIAKVVFATVRGAKDAVQHLHSTSVMGNIIH
VELDT
KGETRMRFYELLVTGRYTPQTLPVGELDAVSPIVNETLQLSDALKRLKDGGLSAGCGSGS
SSVTPNSGGTPFSQDTAYSSCRLDTPNSYGQGTPLTPRLGTPFSQDSSYSSRQPTPSYLF
SQDPAVTFKARRHESKFTDAYNRRHEHHYVHNSPAVTAVAGATAAFRGSSDLPFGAVGGT
GGSSGPPFKAQPQDSATFAHTPPPAQATPAPGFKSAFSPYQTPVAHFPPPPEEPTATAAF
GARDSGEFRRAPAPPPLPPAEPLAKEKPGTPPGPPPPDTNSMELGGRPTFGWSPEPCDSP
GTPTLESSPAGPEKPHDSLDSRIEMLLKEQRTKLLFLREPDSDTELQMEGSPISSSSSQL
SPLAPFGTNSQPGFRGPTPPSSRPSSTGLEDISPTPLPDSDEDEELDLGLGPRPPPEPGP
PDPAGLLSQTAEVALDLVGDRTPTSEKMDEGQQSSGEDMEISDDEMPSAPITSADCPKPM
VVTPGAAAVAAPSVLAPTLPLPPPPGFPPLPPPPPPPPPQPGFPMPPPLPPPPPPPPPAH
PAVTVPPPPLPAPPGVPPPPILPPLPPFPPGLFPVMQVDMSHVLGGQWGGMPMSFQMQTQ
VLSRLMTGQGACPYPPFMAAAAAAASAGLQFVNLPPYRGPFSLSNSGPGRGQHWPPLPKF
DPSVPPPGYMPRQEDPHKATVDGVLLVVLKELKAIMKRDLNRKMVEVVAFRAFDEWWDKK
ERMAKASLTPVKSGEHKDEDRPKPKDRIASCLLESWGKGEGLGYEGLGLGIGLRGAIRLP
SFKVKRKEPPDTTSSGDQKRLRPSTSVDEEDEESERERDRDMADTPCELAKRDPKGVGVR
RRPARPLELDSGGEEDEKESLSASSSSSASSSSGSSTTSPSSSASDKEEEQESTEEEEEA
EEEEEEEVPRSQLSSSSTSSTSDKDDDDDDSDDRDESENDDEDTALSEASEKDEGDSDEE
ETVSIVTSKAEATSSSESSESSEFESSSESSPSSSEDEEEVVAREEEEEEEEEEMVAEES
MASAGPEDFEQDGEEAALAPGAPAVDSLGMEEEVDIETEAVAPEERPSMLDEPPLPVGVE
EPADSREPPEEPGLSQEGAMLLSPEPPAKEVEARPPLSPERAPEHDLEVEPEPPMMLPLP
LQPPLPPPRPPRPPSPPPEPETTDASHPSVPPEPLAEDHPPHTPGLCGSLAKSQSTETVP
ATPGGEPPLSGGSSGLSLSSPQVPGSPFSYPAPSPSLSSGGLPRTPGRDFSFTPTFSEPS
GPLLLPVCPLPTGRRDERSGPLASPVLLETGLPLPLPLPLPLPLALPAVLRAQARAPTPL
PPLLPAPLASCPPPMKRKPGRPRRSPPSMLSLDGPLVRPPAGAALGRELLLLPGQPQTPV
FPSTHDPRTVTLDFRNAGIPAPPPPLPPQPPPPPPPPPVEPTKLPFKELDNQWPSEAIPP
GPRGRDEVTEEYMELAKSRGPWRRPPKKRHEDLVPPAGSPELSPPQPLFRPRSEFEEMTI
LYDIWNGGIDEEDIRFLCVTYERLLQQDNGMDWLNDTLWVYHPSTSLSSAKKKKRDDGIR
EHVTGCARSEGFYTIDKKDKLRYLNSSRASTDEPPADTQGMSIPAQPHASTRAGSERRSE
QRRLLSSFTGSCDSDLLKFNQ
LKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQN
IRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVE
SQKKIVIYSKQHINVNEEITYDYK
FPIEDVKIPCLCGSENCRGTLN
Sequence length 1966
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Lysine degradation
Metabolic pathways
  PKMTs methylate histone lysines
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
21
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
Epilepsy Likely pathogenic rs1592977444 RCV000853296
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual developmental disorder with seizures and language delay Likely pathogenic; Pathogenic rs2137544259, rs2137594297, rs2137553018, rs2137589783, rs2137552415, rs1419959359, rs752096360, rs2137544133, rs2137578021, rs2137588997, rs2500183969, rs2500233324, rs1244562984, rs2500260789, rs2500221145
View all (24 more)
RCV001374426
RCV003224569
RCV001591648
RCV001775333
RCV001780001
View all (35 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neoplasm Pathogenic rs777278685 RCV004673829
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental delay Likely pathogenic; Pathogenic rs2137588997 RCV002274370
★★★★☆
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
AUTOSOMAL DOMINANT NON-SYNDROMIC INTELLECTUAL DISABILITY Disgenet, Orphanet
Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
COMPLEX NEURODEVELOPMENTAL DISORDER ClinGen
★★☆☆☆
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
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 35479077 Associate
★☆☆☆☆
Found in Text Mining only
Autistic behavior Autism BEFREE 31110234
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism BEFREE 29322246
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism Pubtator 34345025 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 30628696 Associate
★☆☆☆☆
Found in Text Mining only
Cardiomyopathy, Familial Idiopathic Cardiomyopathy BEFREE 28805231
★☆☆☆☆
Found in Text Mining only
Colorectal Carcinoma Colorectal Cancer BEFREE 24925220
★☆☆☆☆
Found in Text Mining only
Colorectal Neoplasms Colorectal neoplasm Pubtator 32094334 Associate
★☆☆☆☆
Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma Renal Carcinoma BEFREE 29944950
★☆☆☆☆
Found in Text Mining only
Coronary Artery Disease Coronary artery disease GWASCAT_DG 30525989
★★☆☆☆
Found in Text Mining + Unknown/Other Associations