SETD1A SET domain containing 1A, histone lysine methyltransferase [Homo sapiens (human)] - Gene

Summary

Official Symbol: SETD1Aprovided by HGNC
Official Full Name: SET domain containing 1A, histone lysine methyltransferaseprovided by HGNC
Primary source: HGNC:HGNC:29010
See related: Ensembl:ENSG00000099381 MIM:611052; AllianceGenome:HGNC:29010
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: Set1; EPEDD; EPEO2; KMT2F; Set1A; NEDSID
Summary: The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]
Expression: Ubiquitous expression in testis (RPKM 10.6), bone marrow (RPKM 6.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16p11.2

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (30957754..30984664)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (31344075..31372106)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (30969075..30995985)

Chromosome 16 - NC_000016.10 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?

SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases.
Title: SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases.
In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F).
Title: In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F).
Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
Title: Epigenotype-genotype-phenotype correlations in SETD1A and SETD2 chromatin disorders.
SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3.
Title: SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3.
SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells.
Title: SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells.
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.
SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
Title: SETD1A regulates transcriptional pause release of heme biosynthesis genes in leukemia.
Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway.
Title: Loss-of-function variants in the schizophrenia risk gene SETD1A alter neuronal network activity in human neurons through the cAMP/PKA pathway.
Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis.
Title: Novel missense SETD1A variants in Japanese patients with schizophrenia: Resequencing and association analysis.
Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.
Title: Cell type-specific mechanism of Setd1a heterozygosity in schizophrenia pathogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (58)

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
Epilepsy, early-onset, with or without developmental delay MedGen: C5394228 OMIM: 618832 GeneReviews: Not available	Compare labs
Neurodevelopmental disorder with speech impairment and dysmorphic facies MedGen: C5436699 OMIM: 619056 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-02-28) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2018-02-28) ClinGen Genome Curation PagePubMed

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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Three components (Setd1A, CXXC1, WDR5) of the Set1 histone methyltransferase complex are identified to interact with HIV-1 Tat in Jurkat cell	PubMed

Go to the HIV-1, Human Interaction Database

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	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone H3K4 methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 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 DNA damage response	IEA Inferred from Electronic Annotation more info
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in regulation of chromatin organization	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of hematopoietic stem cell differentiation	IDA Inferred from Direct Assay more info	PubMed

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
part_of Set1C/COMPASS complex	TAS Traceable Author Statement more info	PubMed
part_of chromatin	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: histone-lysine N-methyltransferase SETD1A

Names: SET domain-containing protein 1A; hSET1A; lysine N-methyltransferase 2F; set1/Ash2 histone methyltransferase complex subunit SET1

NP_055527.1

EC 2.1.1.364

XP_005255780.1

EC 2.1.1.364

XP_006721169.1

EC 2.1.1.364

XP_016879398.1

EC 2.1.1.364

XP_024306267.1

EC 2.1.1.364

XP_047290918.1

EC 2.1.1.364

XP_047290919.1

EC 2.1.1.364

XP_047290920.1

EC 2.1.1.364

XP_054170479.1

EC 2.1.1.364

XP_054170480.1

EC 2.1.1.364

XP_054170481.1

EC 2.1.1.364

XP_054170482.1

EC 2.1.1.364

XP_054170483.1

EC 2.1.1.364

XP_054170484.1

EC 2.1.1.364

XP_054170485.1

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.

Genomic

NG_052948.1 RefSeqGene

Range

5461..32371

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_014712.3 → NP_055527.1 histone-lysine N-methyltransferase SETD1A

See identical proteins and their annotated locations for NP_055527.1

Status: REVIEWED

Source sequence(s)

AB002337, BC027450

Consensus CDS

CCDS32435.1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Related

ENSP00000262519.8, ENST00000262519.14

Conserved Domains (5) summary

smart00317
Location:1568 → 1691

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

smart00508
Location:1691 → 1707

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

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1425 → 1562

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

cl26247
Location:1070 → 1130

DNA_pol3_delta2; DNA polymerase III, delta subunit

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_000016.10 Reference GRCh38.p14 Primary Assembly

Range

30957754..30984664

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017023909.2 → XP_016879398.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Conserved Domains (5) summary

smart00317
Location:1568 → 1691

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

smart00508
Location:1691 → 1707

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

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1425 → 1562

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

cl26247
Location:1070 → 1130

DNA_pol3_delta2; DNA polymerase III, delta subunit
XM_005255723.1 → XP_005255780.1 histone-lysine N-methyltransferase SETD1A isoform X1

See identical proteins and their annotated locations for XP_005255780.1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Related

ENSP00000507683.1, ENST00000684162.1

Conserved Domains (5) summary

smart00317
Location:1568 → 1691

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

smart00508
Location:1691 → 1707

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

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1425 → 1562

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

cl26247
Location:1070 → 1130

DNA_pol3_delta2; DNA polymerase III, delta subunit
XM_047434964.1 → XP_047290920.1 histone-lysine N-methyltransferase SETD1A isoform X2
XM_047434962.1 → XP_047290918.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_006721106.4 → XP_006721169.1 histone-lysine N-methyltransferase SETD1A isoform X1

See identical proteins and their annotated locations for XP_006721169.1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Conserved Domains (5) summary

smart00317
Location:1568 → 1691

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

smart00508
Location:1691 → 1707

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

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1425 → 1562

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

cl26247
Location:1070 → 1130

DNA_pol3_delta2; DNA polymerase III, delta subunit
XM_024450499.2 → XP_024306267.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Conserved Domains (5) summary

smart00317
Location:1568 → 1691

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

smart00508
Location:1691 → 1707

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

cd12548
Location:92 → 186

RRM_Set1A; RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A)

pfam11764
Location:1425 → 1562

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

cl26247
Location:1070 → 1130

DNA_pol3_delta2; DNA polymerase III, delta subunit
XM_047434963.1 → XP_047290919.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

31344075..31372106

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314504.1 → XP_054170479.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_054314510.1 → XP_054170485.1 histone-lysine N-methyltransferase SETD1A isoform X2
XM_054314506.1 → XP_054170481.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_054314508.1 → XP_054170483.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_054314507.1 → XP_054170482.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_054314505.1 → XP_054170480.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6
XM_054314509.1 → XP_054170484.1 histone-lysine N-methyltransferase SETD1A isoform X1

UniProtKB/Swiss-Prot

A0A804HLA6, A6NP62, O15047, Q6PIF3, Q8TAJ6