Setd2 MGI Mouse Gene Detail - MGI:1918177

Symbol

Setd2
Name

SET domain containing 2
Synonyms

4921524K10Rik, KMT3A

Feature Type

protein coding gene
IDs

MGI:1918177
NCBI Gene: 235626
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr9:110361665-110447701 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 60.00 cM
Mapping Data

3 experiments

SNPs within 2kb

1833 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918177	protein coding gene	Chr9:110361368-110447703 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0035350	protein coding gene	Chr9:112694623-112784422 (+)
A/J	MGP_AJ_G0035331	protein coding gene	Chr9:108591967-108679037 (+)
AKR/J	MGP_AKRJ_G0035262	protein coding gene	Chr9:111290960-111378661 (+)
BALB/cJ	MGP_BALBcJ_G0035326	protein coding gene	Chr9:108340122-108428081 (+)
C3H/HeJ	MGP_C3HHeJ_G0035034	protein coding gene	Chr9:111799504-111886918 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0035848	protein coding gene	Chr9:115750003-115848053 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032734	protein coding gene	Chr9:105812635-105898660 (+)
CAST/EiJ	MGP_CASTEiJ_G0034340	protein coding gene	Chr9:111588268-111681323 (+)
CBA/J	MGP_CBAJ_G0035001	protein coding gene	Chr9:120064766-120158175 (+)
DBA/2J	MGP_DBA2J_G0035160	protein coding gene	Chr9:108054262-108140210 (+)
FVB/NJ	MGP_FVBNJ_G0035107	protein coding gene	Chr9:106882004-106968421 (+)
LP/J	MGP_LPJ_G0035239	protein coding gene	Chr9:112987029-113077225 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0035147	protein coding gene	Chr9:121403705-121499809 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035868	protein coding gene	Chr9:111627048-111717861 (+)
PWK/PhJ	MGP_PWKPhJ_G0034047	protein coding gene	Chr9:108299592-108386440 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0033882	protein coding gene	Chr9:111708587-111797171 (+)
WSB/EiJ	MGP_WSBEiJ_G0034461	protein coding gene	Chr9:111496491-111585074 (+)

Human Ortholog

SETD2, SET domain containing 2, histone lysine methyltransferase

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SETD2, SET domain containing 2, histone lysine methyltransferase
Synonyms

HBP231, HIF-1, HIP-1, HSPC069, HYPB, KMT3A, LLS, MRD70, p231HBP, RAPAS, SET2
Links

HGNC:18420

NCBI Gene ID: 29072

neXtProt AC: NX_Q9BYW2

UniProt: Q9BYW2
Chr Location

3p21.31; chr3:47016428-47164840 (-) GRCh38

MGI Vertebrate Homology

Setd2 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SETD2
Gene Tree

Setd2

Diseases

8 with human SETD2 associations

				Human Disease	Mouse Models
				autosomal dominant intellectual developmental disorder IDs autosomal dominant intellectual developmental disorder DOID:0060307 OMIM:PS156200 ORDO:178469
				clear cell renal cell carcinoma IDs clear cell renal cell carcinoma DOID:4467 MESH:D002292 NCI:C4033 UMLS_CUI:C0279702
				colorectal cancer IDs colorectal cancer DOID:9256 ICD10CM:C18.9 KEGG:05210 MESH:D015179 NCI:C2956 NCI:C4978 OMIM:114500 UMLS_CUI:C0009404 UMLS_CUI:C0346629
				gastrointestinal stromal tumor IDs gastrointestinal stromal tumor DOID:9253 ICD10CM:C49.A MESH:D046152 NCI:C3868 OMIM:606764 UMLS_CUI:C0238198
				idiopathic pulmonary fibrosis IDs idiopathic pulmonary fibrosis DOID:0050156 EFO:0000768 ICD10CM:J84.112 ICD9CM:516.31 MESH:D054990 NCI:C35716 UMLS_CUI:C1800706
				lung adenocarcinoma IDs lung adenocarcinoma DOID:3910 DOID:4826 EFO:0000571 MESH:D000077192 NCI:C27745 NCI:C3512 UMLS_CUI:C0152013 UMLS_CUI:C1335060
				malignant mesothelioma IDs malignant mesothelioma DOID:1790 DOID:4487 DOID:6965 DOID:7434 MESH:D000086002 NCI:C27926 NCI:C4456 NCI:C7865 NCI:C8420 OMIM:156240 UMLS_CUI:C0278752 UMLS_CUI:C0345967 UMLS_CUI:C0392400 UMLS_CUI:C1332338
				malignant pleural mesothelioma IDs malignant pleural mesothelioma DOID:7474 ICD10CM:C45.0 MESH:D000086002 NCI:C7376 UMLS_CUI:C0812413

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

25 phenotypes from 3 alleles in 3 genetic backgrounds
35 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

32
Endonuclease-mediated

5
Gene trapped

19
Targeted

8
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

102 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit impaired embryonic vascular remodeling in the embryo proper, yolk sac, and placenta that leads to death around E10.5.

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All GO Annotations

67
GO References

14

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

825
Tissues

112
cDNA Data

164
Literature Summary

11

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA SETD2

Xenbase setd2

ZFIN setd2

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All Sequences

79
RefSeq

19
UniProt

7
CCDS

CCDS40781.2

Ensembl

ENSMUSG00000044791 (Evidence)
NCBI Gene

235626

			Length	Strain/Species	Flank
genomic	ENSMUSG00000044791	Ensembl Gene Model \| MGI Sequence Detail	86037	C57BL/6J	± kb
transcript	ENSMUST00000153838	Ensembl \| MGI Sequence Detail	8350	Not Applicable
polypeptide	ENSMUSP00000116313	Ensembl \| MGI Sequence Detail	2537	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000014721 histone-lysine N-methyltransferase SETD2

(term hierarchy)
EC

2.1.1.-, 2.1.1.359
InterPro Domains

IPR006560 AWS domain

IPR042294 Histone-lysine N-methyltransferase SETD2, animal

IPR003616 Post-SET domain

IPR013257 Set2 Rpb1 interacting domain

IPR038190 Set2 Rpb1 interacting domain superfamily

IPR044437 SETD2/Set2, SET domain

IPR001214 SET domain

IPR046341 SET domain superfamily

IPR035441 TFIIS/LEDGF domain superfamily

IPR001202 WW domain

IPR036020 WW domain superfamily
GlyGen

E9Q5F9 1 site, 1 O-linked glycan (1 site)

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All nucleic 166

cDNA 164

Primer pair 2

Microarray probesets 5

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MGI:2446266

Summaries

All 87

Developmental Gene Expression 11

Gene Ontology 14

Phenotypes 35
Earliest

J:106641 Hilditch-Maguire P, et al., Huntingtin: an iron-regulated protein essential for normal nuclear and perinuclear organelles. Hum Mol Genet. 2000 Nov 22;9(19):2789-97
Latest

J:355653 Chen S, et al., Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation. Front Med. 2024 Aug 8;

TSS for Setd2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr87391	Chr9:110361506-110361535 (+)	-144 bp
Tssr87392	Chr9:110361569-110361668 (+)	-46 bp
Tssr87393	Chr9:110361675-110361708 (+)	27 bp
Tssr87394	Chr9:110361710-110361760 (+)	70 bp
Tssr3033	Chr9:110361761-110361796 (+)	114 bp
Tssr87395	Chr9:110376194-110376205 (+)	14,535 bp
Tssr87396	Chr9:110376739-110376776 (+)	15,093 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24