Hmgcs2 MGI Mouse Gene Detail - MGI:101939 - 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2

Symbol

Hmgcs2
Name

3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2
Synonyms

mHS

Feature Type

protein coding gene
IDs

MGI:101939
NCBI Gene: 15360
Alliance

gene page
Transcription Start Sites

16 TSS

Sequence Map

Chr3:98187751-98218054 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 42.74 cM
Mapping Data

7 experiments

SNPs within 2kb

1050 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_101939	protein coding gene	Chr3:98187747-98218054 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027650	protein coding gene	Chr3:99281909-99311111 (+)
A/J	MGP_AJ_G0027612	protein coding gene	Chr3:96095665-96122098 (+)
AKR/J	MGP_AKRJ_G0027579	protein coding gene	Chr3:98395653-98424796 (+)
BALB/cJ	MGP_BALBcJ_G0027622	protein coding gene	Chr3:95892600-95918732 (+)
C3H/HeJ	MGP_C3HHeJ_G0027354	protein coding gene	Chr3:98660476-98686882 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028068	protein coding gene	Chr3:102948857-102978687 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025410	protein coding gene	Chr3:92333204-92357953 (+)
CAST/EiJ	MGP_CASTEiJ_G0026809	protein coding gene	Chr3:97968972-97996974 (+)
CBA/J	MGP_CBAJ_G0027329	protein coding gene	Chr3:106621124-106655430 (+)
DBA/2J	MGP_DBA2J_G0027472	protein coding gene	Chr3:95398992-95425133 (+)
FVB/NJ	MGP_FVBNJ_G0027441	protein coding gene	Chr3:93394310-93423545 (+)
LP/J	MGP_LPJ_G0027577	protein coding gene	Chr3:100544948-100571331 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027467	protein coding gene	Chr3:112684599-112710479 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028122	protein coding gene	Chr3:98014724-98040862 (+)
PWK/PhJ	MGP_PWKPhJ_G0026534	protein coding gene	Chr3:95298048-95324379 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026356	protein coding gene	Chr3:96294762-96321066 (+)
WSB/EiJ	MGP_WSBEiJ_G0026887	protein coding gene	Chr3:98461552-98487768 (+)

Human Ortholog

HMGCS2, 3-hydroxy-3-methylglutaryl-CoA synthase 2

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

HMGCS2, 3-hydroxy-3-methylglutaryl-CoA synthase 2
Links

HGNC:5008

NCBI Gene ID: 3158

neXtProt AC: NX_P54868

UniProt: P54868
Chr Location

1p12; chr1:119747996-119768932 (-) GRCh38

MGI Vertebrate Homology

Hmgcs2 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: HMGCS2
Gene Tree

Hmgcs2

Diseases

1 with Hmgcs2 mouse models; 1 with human HMGCS2 associations

Human Disease

Mouse Models

HMG-CoA synthase 2 deficiency

IDs

View 2 models

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

Mutations/Alleles

1 with disease annotations

References

2 with disease annotations

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Phenotype Summary

17 phenotypes from 3 alleles in 2 genetic backgrounds
1 phenotype from multigenic genotypes
22 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

17
Chemically induced (other)

1
Endonuclease-mediated

10
Radiation induced

1
Targeted

5
Genomic Mutations

2 involving Hmgcs2
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

33 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a null allele exhibit increased postnatal lethality, decreased weight but increased body fat mass, hepatic steatosis, and impaired ketogenesis during P0 to P14 growth, with no increase in ketone levels.

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All GO Annotations

47
GO References

12

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

1289
Tissues

240
cDNA Data

17
Literature Summary

22

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

42
RefSeq

2
UniProt

2
CCDS

CCDS17662.1

Ensembl

ENSMUSG00000027875 (Evidence)
NCBI Gene

15360

			Length	Strain/Species	Flank
genomic	ENSMUSG00000027875	Ensembl Gene Model \| MGI Sequence Detail	30304	C57BL/6J	± kb
transcript	ENSMUST00000120541	Ensembl \| MGI Sequence Detail	2524	Not Applicable
polypeptide	ENSMUSP00000113296	Ensembl \| MGI Sequence Detail	508	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000008638 hydroxymethylglutaryl-CoA synthase, mitochondrial

(term hierarchy)
EC

2.3.3.10
InterPro Domains

IPR010122 Hydroxymethylglutaryl-CoA synthase, eukaryotic

IPR000590 Hydroxymethylglutaryl-coenzyme A synthase, active site

IPR013746 Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain

IPR013528 Hydroxymethylglutaryl-coenzyme A synthase, N-terminal

IPR016039 Thiolase-like
GlyGen

P54869 2 sites, 1 O-linked glycan (2 sites)

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All nucleic 19

cDNA 17

Primer pair 2

Microarray probesets 4

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MGD-MRK-18773

Summaries

All 83

Developmental Gene Expression 22

Diseases 2

Gene Ontology 12

Phenotypes 22
Earliest

J:17114 Valera A, et al., Overexpression of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase in transgenic mice causes hepatic hyperketogenesis. J Biol Chem. 1994 Mar 4;269(9):6267-70
Latest

J:343296 Ma W, et al., Metabolic regulation in erythroid differentiation by systemic ketogenesis in fasted mice. Exp Hematol. 2023 Oct 26;

TSS for Hmgcs2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr30829	Chr3:98187246-98187268 (+)	-494 bp
Tssr30830	Chr3:98187346-98187352 (+)	-402 bp
Tssr30831	Chr3:98187743-98187760 (+)	1 bp
Tssr30832	Chr3:98188791-98188808 (+)	1,049 bp
Tssr30834	Chr3:98198207-98198223 (+)	10,464 bp
Tssr30835	Chr3:98198431-98198442 (+)	10,686 bp
Tssr30836	Chr3:98198567-98198580 (+)	10,823 bp
Tssr30837	Chr3:98198600-98198615 (+)	10,857 bp
Tssr30838	Chr3:98206424-98206447 (+)	18,685 bp
Tssr30839	Chr3:98206487-98206494 (+)	18,740 bp
Tssr30840	Chr3:98206522-98206542 (+)	18,781 bp
Tssr30841	Chr3:98209925-98209953 (+)	22,188 bp
Tssr30842	Chr3:98216339-98216358 (+)	28,598 bp
Tssr30843	Chr3:98216404-98216415 (+)	28,659 bp
Tssr30844	Chr3:98216471-98216485 (+)	28,727 bp
Tssr30845	Chr3:98217340-98217362 (+)	29,600 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)
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