SETD1B SET domain containing 1B, histone lysine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SETD1Bprovided by HGNC
Official Full Name: SET domain containing 1B, histone lysine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:29187
See related: Ensembl:ENSG00000139718 MIM:611055; AllianceGenome:HGNC:29187
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KMT2G; Set1B; IDDSELD
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]
Expression: Ubiquitous expression in endometrium (RPKM 7.9), spleen (RPKM 6.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.31

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (121790155..121832656)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (121800295..121829318)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (122241915..122270562)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypic spectrum of SETD1B-related disorder: Myoclonic absence seizures and concurrent intellectual disability - Insights from two cases.
Title: Phenotypic spectrum of SETD1B-related disorder: Myoclonic absence seizures and concurrent intellectual disability - Insights from two cases.
Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
Title: Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82.
Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.
Title: Delineating the molecular and phenotypic spectrum of the SETD1B-related syndrome.
SETD1B-associated neurodevelopmental disorder.
Title: SETD1B-associated neurodevelopmental disorder.
Study identify a specific hypermethylation signature associated with loss of function mutations in the SETD1B gene which may be used as an epigenetic marker supporting the diagnosis of syndromic SETD1B-related diseases.
Title: A genome-wide DNA methylation signature for SETD1B-related syndrome.
Results show that SETD1B is the most frequently mutated gene along with TP53 in primary hepatic neuroendocrine tumors (PHNETs). A biological analysis suggests that one of the three SETD1B mutants, A1054del, promotes cell proliferation, migration and invasion compared to wild-type SETD1B. Our work unveils that SETD1B A1054del mutant is functional in PHNET and implicates this gene on PHNET pathogenesis.
Title: SET domain containing 1B gene is mutated in primary hepatic neuroendocrine tumors.
we report a first epilepsy patient with a frameshift variant in SETD1B, emphasizing a possible pathomechanistic association of SETD1B abnormality with neurodevelopmental delay with epilepsy.
Title: A novel de novo frameshift variant in SETD1B causes epilepsy.
the results demonstrated that SETD1B is essential in the progression of hepatocellular carcinoma and may be used as a potential prognostic marker and therapeutic target in hepatocellular carcinoma.
Title: High‑level SETD1B gene expression is associated with unfavorable prognosis in hepatocellular carcinoma.
SETD1B aberration is likely to be the core defect in 12q24.3 deletion syndrome.
Title: De novo variants in SETD1B are associated with intellectual disability, epilepsy and autism.
KMT2G levels were higher in metastatic clear cell renal cell carcinomas and may be a good marker for discriminating metastatic tumors from non-metastatic tumors.
Title: Expression and clinical significance of COMPASS family of histone methyltransferases in clear cell renal cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual developmental disorder with seizures and language delay MedGen: C5436574 OMIM: 619000 GeneReviews: SETD1B-Related Neurodevelopmental Disorder	Compare labs

EBI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of SET domain containing 1B (SETD1B) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables histone H3 methyltransferase activity	TAS Traceable Author Statement more info
contributes_to histone H3K4 methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H3K4 monomethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables histone H3K4 trimethyltransferase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Set1C/COMPASS complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Set1C/COMPASS complex	IDA Inferred from Direct Assay more info	PubMed
part_of Set1C/COMPASS complex	IPI Inferred from Physical Interaction more info	PubMed
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of histone methyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD1B

Names: SET domain-containing protein 1B; lysine N-methyltransferase 2G

NP_001340274.1

EC 2.1.1.364

XP_024304666.1

EC 2.1.1.364

XP_047284508.1

EC 2.1.1.364

XP_047284509.1

EC 2.1.1.364

XP_054227457.1

EC 2.1.1.364

XP_054227458.1

EC 2.1.1.364

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001353345.2 → NP_001340274.1 histone-lysine N-methyltransferase SETD1B

Status: REVIEWED

Source sequence(s)

AC079360, AC084018

Consensus CDS

CCDS86338.1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6

Related

ENSP00000474253.1, ENST00000604567.6

Conserved Domains (5) summary

smart00317
Location:1834 → 1949

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

smart00508
Location:1950 → 1966

PostSET; Cysteine-rich motif following a subset of SET domains

cd12549
Location:101 → 193

RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

pfam11764
Location:1679 → 1821

N-SET; COMPASS (Complex proteins associated with Set1p) component N

cl25865
Location:1237 → 1308

Trypan_PARP; Procyclic acidic repetitive protein (PARP)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

121790155..121832656

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047428553.1 → XP_047284509.1 histone-lysine N-methyltransferase SETD1B isoform X1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6
XM_024448898.2 → XP_024304666.1 histone-lysine N-methyltransferase SETD1B isoform X1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6

Conserved Domains (5) summary

smart00317
Location:1834 → 1949

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

smart00508
Location:1950 → 1966

PostSET; Cysteine-rich motif following a subset of SET domains

cd12549
Location:101 → 193

RRM_Set1B; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B)

pfam11764
Location:1679 → 1821

N-SET; COMPASS (Complex proteins associated with Set1p) component N

cl25865
Location:1237 → 1308

Trypan_PARP; Procyclic acidic repetitive protein (PARP)
XM_047428552.1 → XP_047284508.1 histone-lysine N-methyltransferase SETD1B isoform X1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6

Related

ENSP00000481531.1, ENST00000619791.1

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

121800295..121829318

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054371482.1 → XP_054227457.1 histone-lysine N-methyltransferase SETD1B isoform X1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6
XM_054371483.1 → XP_054227458.1 histone-lysine N-methyltransferase SETD1B isoform X1

UniProtKB/Swiss-Prot

F6MFW1, Q9UPS6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_015048.1: Suppressed sequence

Description

NM_015048.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.