HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: HMGCS2 (3-hydroxy-3-methylglutaryl-CoA synthase 2) Homo sapiens
Analyze
Symbol: HMGCS2
Name: 3-hydroxy-3-methylglutaryl-CoA synthase 2
RGD ID: 737571
HGNC Page HGNC
Description: Exhibits hydroxymethylglutaryl-CoA synthase activity and identical protein binding activity. Involved in acetyl-CoA metabolic process and ketone body biosynthetic process. Localizes to mitochondrion. Biomarker of hepatocellular carcinoma.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: 3-hydroxy-3-methylglutaryl coenzyme A synthase; 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial); 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial); HMG-CoA synthase; hydroxymethylglutaryl-CoA synthase, mitochondrial; mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase; testicular tissue protein Li 88
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1119,748,002 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1119,747,996 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh381119,747,996 - 119,768,932 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371120,290,619 - 120,311,555 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,092,525 - 120,113,041 (-)NCBINCBI36hg18NCBI36
Build 341120,003,046 - 120,023,560NCBI
Celera1118,521,355 - 118,542,283 (-)NCBI
Cytogenetic Map1p12NCBI
HuRef1118,149,159 - 118,170,093 (-)NCBIHuRef
CHM1_11120,406,161 - 120,427,088 (-)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (EXP)
(+)-dexrazoxane  (ISO)
(+)-schisandrin B  (ISO)
1,2-dimethylhydrazine  (ISO)
1-benzylpiperazine  (ISO)
14-Deoxy-11,12-didehydroandrographolide  (EXP)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)propanoic acid  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (ISO)
3-hydroxybutyric acid  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (ISO)
acetamide  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
ammonium chloride  (ISO)
Aroclor 1254  (ISO)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzo[k]fluoranthene  (ISO)
bezafibrate  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (ISO)
bromobenzene  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
calcium atom  (ISO)
calcium(0)  (ISO)
captan  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (ISO)
cefaloridine  (ISO)
cetrorelix  (EXP)
chenodeoxycholic acid  (EXP)
chlorpyrifos  (ISO)
ciglitazone  (EXP)
ciguatoxin CTX1B  (ISO)
ciprofibrate  (ISO)
clofibrate  (ISO)
Clofop  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
corticosterone  (ISO)
cyclosporin A  (EXP,ISO)
cytarabine  (EXP)
desogestrel  (EXP)
dexamethasone  (ISO)
dichlorine  (ISO)
dichloroacetic acid  (ISO)
diclofenac  (ISO)
diuron  (ISO)
dopamine  (ISO)
dorsomorphin  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP,ISO)
entinostat  (EXP)
ethanol  (ISO)
fenofibrate  (EXP,ISO)
fenoldopam  (ISO)
fipronil  (EXP,ISO)
flutamide  (ISO)
folic acid  (ISO)
folpet  (ISO)
fructose  (ISO)
fumonisin B1  (ISO)
furan  (ISO)
gadolinium trichloride  (ISO)
gemfibrozil  (ISO)
genistein  (ISO)
glafenine  (ISO)
glyphosate  (ISO)
GW 4064  (EXP)
GW 501516  (EXP)
GW 7647  (EXP,ISO)
Heptachlor epoxide  (ISO)
hydrazine  (ISO)
indometacin  (ISO)
iron atom  (ISO)
iron(0)  (ISO)
ketamine  (ISO)
lamivudine  (ISO)
lead diacetate  (ISO)
lithocholic acid  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
menadione  (EXP)
methapyrilene  (ISO)
methimazole  (ISO)
methotrexate  (ISO)
morphine  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (ISO)
N-nitrosomorpholine  (ISO)
N-Nitrosopyrrolidine  (EXP)
nevirapine  (ISO)
nickel atom  (EXP)
nickel dichloride  (ISO)
O-methyleugenol  (EXP)
oxybenzone  (ISO)
ozone  (ISO)
p-toluidine  (ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
perfluorodecanoic acid  (EXP)
perfluorododecanoic acid  (EXP)
perfluoroheptanoic acid  (EXP)
perfluorohexanesulfonic acid  (EXP)
perfluorononanoic acid  (EXP)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (EXP,ISO)
phenethyl caffeate  (ISO)
phenobarbital  (ISO)
PhIP  (ISO)
pirinixic acid  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
prostaglandin F2alpha  (ISO)
pyrazinecarboxamide  (ISO)
pyrrolidine dithiocarbamate  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 431542  (EXP)
sodium arsenite  (EXP,ISO)
sodium dichromate  (ISO)
streptozocin  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
tebuconazole  (EXP)
Tesaglitazar  (ISO)
testosterone enanthate  (EXP)
Tetrachlorobisphenol A  (EXP)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
tetracycline  (ISO)
tetrathiomolybdate(2-)  (ISO)
thiacloprid  (ISO)
thioacetamide  (ISO)
thiophanate-methyl  (ISO)
titanium dioxide  (ISO)
tributylstannane  (ISO)
trichloroethene  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
troglitazone  (ISO)
urethane  (EXP)
ursodeoxycholic acid  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc sulfate  (EXP)
zinc(0)  (ISO)
ziram  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
mitochondrial matrix  (ISO,TAS)
mitochondrion  (IBA,IDA)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

Additional References at PubMed
PMID:6986618   PMID:7851882   PMID:7893153   PMID:9305755   PMID:11228257   PMID:11479731   PMID:12477932   PMID:12647205   PMID:15489334   PMID:16940161   PMID:17387528   PMID:18636124  
PMID:18660489   PMID:19913121   PMID:20346956   PMID:20549515   PMID:20618440   PMID:20628086   PMID:20877624   PMID:21502324   PMID:21832049   PMID:21873635   PMID:21952825   PMID:22496890  
PMID:23751782   PMID:23943793   PMID:25389781   PMID:25929810   PMID:27503909   PMID:27816970   PMID:28320515   PMID:28514442   PMID:28676675   PMID:28888048   PMID:29523524   PMID:30021884  
PMID:30097533   PMID:30567295   PMID:31176575   PMID:31355161   PMID:31546785   PMID:31910233   PMID:32259399  


Genomics

Comparative Map Data
HMGCS2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1119,748,002 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1119,747,996 - 119,768,905 (-)EnsemblGRCh38hg38GRCh38
GRCh381119,747,996 - 119,768,932 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371120,290,619 - 120,311,555 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361120,092,525 - 120,113,041 (-)NCBINCBI36hg18NCBI36
Build 341120,003,046 - 120,023,560NCBI
Celera1118,521,355 - 118,542,283 (-)NCBI
Cytogenetic Map1p12NCBI
HuRef1118,149,159 - 118,170,093 (-)NCBIHuRef
CHM1_11120,406,161 - 120,427,088 (-)NCBICHM1_1
Hmgcs2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39398,187,747 - 98,218,054 (+)NCBIGRCm39mm39
GRCm39 Ensembl398,187,751 - 98,218,054 (+)Ensembl
GRCm38398,280,431 - 98,310,738 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl398,280,435 - 98,310,738 (+)EnsemblGRCm38mm10GRCm38
MGSCv37398,084,354 - 98,114,661 (+)NCBIGRCm37mm9NCBIm37
MGSCv36398,365,840 - 98,396,137 (+)NCBImm8
Celera399,679,562 - 99,709,869 (+)NCBICelera
Cytogenetic Map3F2.2NCBI
cM Map342.74NCBI
Hmgcs2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22185,875,609 - 185,903,505 (+)NCBI
Rnor_6.0 Ensembl2200,452,624 - 200,479,423 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02200,452,623 - 200,480,785 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02219,928,546 - 219,956,233 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42193,128,736 - 193,143,106 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12193,091,489 - 193,105,860 (+)NCBI
Celera2178,363,353 - 178,390,245 (+)NCBICelera
Cytogenetic Map2q34NCBI
Hmgcs2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543522,804,484 - 22,821,482 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543522,804,484 - 22,820,807 (-)NCBIChiLan1.0ChiLan1.0
HMGCS2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11117,776,165 - 117,796,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1117,775,770 - 117,796,679 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0182,778,489 - 82,798,987 (+)NCBIMhudiblu_PPA_v0panPan3
HMGCS2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11756,679,942 - 56,698,521 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1756,680,301 - 56,698,419 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1756,315,432 - 56,328,270 (-)NCBI
ROS_Cfam_1.01757,558,992 - 57,577,456 (-)NCBI
UMICH_Zoey_3.11756,594,625 - 56,613,171 (-)NCBI
UNSW_CanFamBas_1.01756,620,825 - 56,639,082 (-)NCBI
UU_Cfam_GSD_1.01757,237,948 - 57,256,436 (-)NCBI
Hmgcs2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505810,015,851 - 10,037,163 (+)NCBI
SpeTri2.0NW_0049366274,451,847 - 4,473,163 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110260333
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4101,385,512 - 101,443,405 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14101,385,486 - 101,404,273 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
HMGCS2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12014,018,669 - 14,040,934 (+)NCBI
ChlSab1.1 Ensembl2014,019,692 - 14,041,016 (+)Ensembl
Hmgcs2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477215,432,612 - 15,464,343 (+)NCBI

Position Markers
RH11689  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371120,291,058 - 120,291,251UniSTSGRCh37
Build 361120,092,581 - 120,092,774RGDNCBI36
Celera1118,521,794 - 118,521,987RGD
Cytogenetic Map1p13-p12UniSTS
HuRef1118,149,598 - 118,149,791UniSTS
D1S3445  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371120,291,117 - 120,291,460UniSTSGRCh37
Build 361120,092,640 - 120,092,983RGDNCBI36
Celera1118,521,853 - 118,522,196RGD
Cytogenetic Map1p13-p12UniSTS
HuRef1118,149,657 - 118,150,000UniSTS
Whitehead-YAC Contig Map1 UniSTS
GeneMap99-G3 RH Map15583.0UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1502
Count of miRNA genes:639
Interacting mature miRNAs:702
Transcripts:ENST00000369406, ENST00000472375, ENST00000476640, ENST00000544913
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 12 167 167 167 2
Medium 847 252 271 389 123 261 840 248 3 247 583 35 129 1 18 509 1 1
Low 560 629 404 55 219 22 1042 807 105 82 288 527 35 239 694 2
Below cutoff 907 1605 788 8 717 8 1713 1012 2780 31 429 770 1 768 1180 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_013348 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001166107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_005518 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011541313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH005575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AI215948 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK301594 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK302276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK303777 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313590 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL589734 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC044217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BF964973 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP420631 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX104280 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471122 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR456850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GU433940 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HM005401 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U12788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U12789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X83618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000369406   ⟹   ENSP00000358414
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1119,748,002 - 119,768,905 (-)Ensembl
RefSeq Acc Id: ENST00000472375
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1119,755,427 - 119,759,414 (-)Ensembl
RefSeq Acc Id: ENST00000476640
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1119,755,488 - 119,764,626 (-)Ensembl
RefSeq Acc Id: ENST00000544913   ⟹   ENSP00000439495
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1119,748,384 - 119,768,905 (-)Ensembl
RefSeq Acc Id: NM_001166107   ⟹   NP_001159579
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381119,747,996 - 119,768,932 (-)NCBI
GRCh371120,290,619 - 120,311,555 (-)ENTREZGENE
HuRef1118,149,159 - 118,170,093 (-)ENTREZGENE
CHM1_11120,406,161 - 120,427,088 (-)NCBI
Sequence:
RefSeq Acc Id: NM_005518   ⟹   NP_005509
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381119,748,002 - 119,768,905 (-)NCBI
GRCh371120,290,619 - 120,311,555 (-)ENTREZGENE
Build 361120,092,525 - 120,113,041 (-)NCBI Archive
HuRef1118,149,159 - 118,170,093 (-)ENTREZGENE
CHM1_11120,406,161 - 120,427,088 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011541313   ⟹   XP_011539615
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381119,748,376 - 119,768,908 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001159579   ⟸   NM_001166107
- Peptide Label: isoform 2 precursor
- UniProtKB: P54868 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_005509   ⟸   NM_005518
- Peptide Label: isoform 1 precursor
- UniProtKB: P54868 (UniProtKB/Swiss-Prot),   A0A140VJL2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011539615   ⟸   XM_011541313
- Peptide Label: isoform X1
- UniProtKB: P54868 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000439495   ⟸   ENST00000544913
RefSeq Acc Id: ENSP00000358414   ⟸   ENST00000369406
Protein Domains
HMG_CoA_synt_C   HMG_CoA_synt_N

Promoters
RGD ID:6856792
Promoter ID:EPDNEW_H1561
Type:multiple initiation site
Name:HMGCS2_1
Description:3-hydroxy-3-methylglutaryl-CoA synthase 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381119,768,905 - 119,768,965EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001166107.1(HMGCS2):c.952T>G (p.Ser318Ala) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000554427] Chr1:119755536 [GRCh38]
Chr1:120298159 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.520T>C (p.Phe174Leu) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009839] Chr1:119764211 [GRCh38]
Chr1:120306834 [GRCh37]
Chr1:1p12
pathogenic|uncertain significance
NM_001166107.1(HMGCS2):c.1144C>T (p.Arg382Ter) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009840] Chr1:119753304 [GRCh38]
Chr1:120295927 [GRCh37]
Chr1:1p12
pathogenic|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.560-633G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009841]|not provided [RCV000498667] Chr1:119759915 [GRCh38]
Chr1:120302538 [GRCh37]
Chr1:1p12
pathogenic|likely pathogenic|conflicting interpretations of pathogenicity
NM_001166107.1(HMGCS2):c.1373G>A (p.Arg458His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009842] Chr1:119750830 [GRCh38]
Chr1:120293453 [GRCh37]
Chr1:1p12
pathogenic|likely pathogenic|conflicting interpretations of pathogenicity
NM_001166107.1(HMGCS2):c.160G>A (p.Val54Met) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009843] Chr1:119764571 [GRCh38]
Chr1:120307194 [GRCh37]
Chr1:1p12
pathogenic|uncertain significance
NM_001166107.1(HMGCS2):c.500A>G (p.Tyr167Cys) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000009844] Chr1:119764231 [GRCh38]
Chr1:120306854 [GRCh37]
Chr1:1p12
pathogenic
GRCh38/hg38 1p13.1-12(chr1:116059621-120130051)x3 copy number gain See cases [RCV000051831] Chr1:116059621..120130051 [GRCh38]
Chr1:116602242..120672637 [GRCh37]
Chr1:116403765..120474160 [NCBI36]
Chr1:1p13.1-12
pathogenic
NM_001166107.1(HMGCS2):c.1059C>T (p.Ser353=) single nucleotide variant Malignant melanoma [RCV000064049] Chr1:119755429 [GRCh38]
Chr1:120298052 [GRCh37]
Chr1:120099575 [NCBI36]
Chr1:1p12
not provided
NM_005518.4(HMGCS2):c.*6-16T>C single nucleotide variant not specified [RCV000125368] Chr1:119748857 [GRCh38]
Chr1:120291480 [GRCh37]
Chr1:1p12
benign
GRCh38/hg38 1p12(chr1:118752239-119977596)x3 copy number gain See cases [RCV000140044] Chr1:118752239..119977596 [GRCh38]
Chr1:119294862..120520219 [GRCh37]
Chr1:119096385..120321742 [NCBI36]
Chr1:1p12
likely benign
GRCh38/hg38 1p21.1-12(chr1:104325484-119977655)x3 copy number gain See cases [RCV000142953] Chr1:104325484..119977655 [GRCh38]
Chr1:104868106..120471049 [GRCh37]
Chr1:104669629..120321801 [NCBI36]
Chr1:1p21.1-12
pathogenic
GRCh38/hg38 1p12(chr1:118933857-119977655)x1 copy number loss See cases [RCV000143206] Chr1:118933857..119977655 [GRCh38]
Chr1:119476480..120471049 [GRCh37]
Chr1:119278003..120321801 [NCBI36]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.73C>G (p.Pro25Ala) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000647361]|not specified [RCV000185971] Chr1:119768772 [GRCh38]
Chr1:120311395 [GRCh37]
Chr1:1p12
likely benign|uncertain significance
NM_001166107.1(HMGCS2):c.364G>A (p.Asp122Asn) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099372]|not provided [RCV000185973] Chr1:119764367 [GRCh38]
Chr1:120306990 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.736C>A (p.Arg246=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000392896]|not specified [RCV000431451] Chr1:119757427 [GRCh38]
Chr1:120300050 [GRCh37]
Chr1:1p12
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.1387C>T (p.Arg463Trp) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000402158] Chr1:119750816 [GRCh38]
Chr1:120293439 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.346C>T (p.Arg116Cys) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000697575]|not provided [RCV000185972] Chr1:119764385 [GRCh38]
Chr1:120307008 [GRCh37]
Chr1:1p12
likely pathogenic|uncertain significance
NM_001166107.1(HMGCS2):c.560-580T>A single nucleotide variant not provided [RCV000185974] Chr1:119759862 [GRCh38]
Chr1:120302485 [GRCh37]
Chr1:1p12
pathogenic|likely pathogenic
NM_001166107.1(HMGCS2):c.1294+13T>C single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000284565] Chr1:119752536 [GRCh38]
Chr1:120295159 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.275G>A (p.Arg92His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000262956] Chr1:119764456 [GRCh38]
Chr1:120307079 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.26A>G (p.Lys9Arg) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000289757] Chr1:119768819 [GRCh38]
Chr1:120311442 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.88C>G (p.Pro30Ala) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000381823] Chr1:119768757 [GRCh38]
Chr1:120311380 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.725-14G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000369940]|not specified [RCV000442121] Chr1:119757452 [GRCh38]
Chr1:120300075 [GRCh37]
Chr1:1p12
likely benign|uncertain significance
NM_001166107.1(HMGCS2):c.736C>T (p.Arg246Ter) single nucleotide variant not provided [RCV000369998] Chr1:119757427 [GRCh38]
Chr1:120300050 [GRCh37]
Chr1:1p12
pathogenic
NM_001166107.1(HMGCS2):c.174C>T (p.Ala58=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000372694]|not provided [RCV000970538]|not specified [RCV000437286] Chr1:119764557 [GRCh38]
Chr1:120307180 [GRCh37]
Chr1:1p12
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.998C>G (p.Ser333Cys) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000364022]|not provided [RCV000418713]|not specified [RCV000607592] Chr1:119755490 [GRCh38]
Chr1:120298113 [GRCh37]
Chr1:1p12
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.646del (p.Ser216fs) deletion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000578257] Chr1:119759196 [GRCh38]
Chr1:120301819 [GRCh37]
Chr1:1p12
pathogenic
NM_001166107.1(HMGCS2):c.175C>A (p.Leu59Met) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099374]|not provided [RCV000756247] Chr1:119764556 [GRCh38]
Chr1:120307179 [GRCh37]
Chr1:1p12
likely benign|uncertain significance
NM_001166107.1(HMGCS2):c.95C>T (p.Ala32Val) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000348168] Chr1:119768750 [GRCh38]
Chr1:120311373 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.732C>T (p.Ser244=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000315225]|not specified [RCV000596891] Chr1:119757431 [GRCh38]
Chr1:120300054 [GRCh37]
Chr1:1p12
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.1396G>A (p.Val466Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000342894]|not provided [RCV000756249] Chr1:119750807 [GRCh38]
Chr1:120293430 [GRCh37]
Chr1:1p12
likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.270G>A (p.Gln90=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000315699]|not specified [RCV000424075] Chr1:119764461 [GRCh38]
Chr1:120307084 [GRCh37]
Chr1:1p12
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.1293G>A (p.Lys431=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000339641]|not specified [RCV000419883] Chr1:119752550 [GRCh38]
Chr1:120295173 [GRCh37]
Chr1:1p12
benign|likely benign
NM_001166107.1(HMGCS2):c.1110T>C (p.Tyr370=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000309230] Chr1:119753338 [GRCh38]
Chr1:120295961 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.560-672G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000355387] Chr1:119759954 [GRCh38]
Chr1:120302577 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.*6-11_*6-8del deletion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000278550] Chr1:119748849..119748852 [GRCh38]
Chr1:120291472..120291475 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.-36T>G single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000401857] Chr1:119768880 [GRCh38]
Chr1:120311503 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.-11C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000351672]|not specified [RCV000609842] Chr1:119768855 [GRCh38]
Chr1:120311478 [GRCh37]
Chr1:1p12
benign|likely benign
NM_001166107.1(HMGCS2):c.*78A>G single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000372865] Chr1:119748769 [GRCh38]
Chr1:120291392 [GRCh37]
Chr1:1p12
likely benign|uncertain significance
NM_001166107.1(HMGCS2):c.560-646C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000273632] Chr1:119759928 [GRCh38]
Chr1:120302551 [GRCh37]
Chr1:1p12
conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.1376G>C (p.Arg459Pro) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000805374]|not provided [RCV000522718] Chr1:119750827 [GRCh38]
Chr1:120293450 [GRCh37]
Chr1:1p12
conflicting interpretations of pathogenicity|uncertain significance
NM_001166107.1(HMGCS2):c.560-650G>A single nucleotide variant not provided [RCV000488182] Chr1:119759932 [GRCh38]
Chr1:120302555 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.241G>A (p.Ala81Thr) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001065755]|not provided [RCV000490124] Chr1:119764490 [GRCh38]
Chr1:120307113 [GRCh37]
Chr1:1p12
uncertain significance
NM_006623.3(PHGDH):c.*200A>G single nucleotide variant Phosphoglycerate dehydrogenase deficiency [RCV000309107]|mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000269827] Chr1:119744240 [GRCh38]
Chr1:120286863 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.*165C>T single nucleotide variant Phosphoglycerate dehydrogenase deficiency [RCV000273781]|mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000318481] Chr1:119748682 [GRCh38]
Chr1:120291305 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.*332A>C single nucleotide variant Phosphoglycerate dehydrogenase deficiency [RCV000366088]|mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000282093] Chr1:119748515 [GRCh38]
Chr1:120291138 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.1036G>A (p.Gly346Arg) single nucleotide variant not provided [RCV000520978] Chr1:119755452 [GRCh38]
Chr1:120298075 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.*792G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099263] Chr1:119748055 [GRCh38]
Chr1:120290678 [GRCh37]
Chr1:1p12
benign
NM_001166107.1(HMGCS2):c.358C>A (p.Pro120Thr) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001210292]|not provided [RCV000732849] Chr1:119764373 [GRCh38]
Chr1:120306996 [GRCh37]
Chr1:1p12
uncertain significance
GRCh37/hg19 1p13.2-12(chr1:114507501-120494232)x3 copy number gain See cases [RCV000449311] Chr1:114507501..120494232 [GRCh37]
Chr1:1p13.2-12
pathogenic
NM_001166107.1(HMGCS2):c.35T>C (p.Leu12Pro) single nucleotide variant not provided [RCV000441706] Chr1:119768810 [GRCh38]
Chr1:120311433 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.560-670C>T single nucleotide variant not specified [RCV000435165] Chr1:119759952 [GRCh38]
Chr1:120302575 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.1185G>A (p.Lys395=) single nucleotide variant not specified [RCV000435485] Chr1:119752658 [GRCh38]
Chr1:120295281 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.560-697C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000888818]|not specified [RCV000428846] Chr1:119759979 [GRCh38]
Chr1:120302602 [GRCh37]
Chr1:1p12
likely benign|conflicting interpretations of pathogenicity
NM_001166107.1(HMGCS2):c.687A>G (p.Thr229=) single nucleotide variant not provided [RCV000916916]|not specified [RCV000429542] Chr1:119759155 [GRCh38]
Chr1:120301778 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.435C>T (p.Leu145=) single nucleotide variant not specified [RCV000422925] Chr1:119764296 [GRCh38]
Chr1:120306919 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.891-18C>T single nucleotide variant not specified [RCV000423205] Chr1:119755615 [GRCh38]
Chr1:120298238 [GRCh37]
Chr1:1p12
likely benign
GRCh37/hg19 1p12(chr1:119806427-120438201)x3 copy number gain See cases [RCV000448151] Chr1:119806427..120438201 [GRCh37]
Chr1:1p12
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NM_001166107.1(HMGCS2):c.891-2del deletion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000578418] Chr1:119755599 [GRCh38]
Chr1:120298222 [GRCh37]
Chr1:1p12
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NM_001166107.1(HMGCS2):c.725-19T>C single nucleotide variant not specified [RCV000612653] Chr1:119757457 [GRCh38]
Chr1:120300080 [GRCh37]
Chr1:1p12
likely benign
GRCh37/hg19 1p22.1-11.2(chr1:93837992-121343783)x3 copy number gain See cases [RCV000512354] Chr1:93837992..121343783 [GRCh37]
Chr1:1p22.1-11.2
pathogenic
NM_001166107.1(HMGCS2):c.399C>G (p.Thr133=) single nucleotide variant not specified [RCV000604764] Chr1:119764332 [GRCh38]
Chr1:120306955 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.1299T>C (p.Asn433=) single nucleotide variant not provided [RCV000647362] Chr1:119750904 [GRCh38]
Chr1:120293527 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.347G>A (p.Arg116His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000700818] Chr1:119764384 [GRCh38]
Chr1:120307007 [GRCh37]
Chr1:1p12
uncertain significance
GRCh37/hg19 1p12(chr1:120294903-120527495)x3 copy number gain not provided [RCV000684619] Chr1:120294903..120527495 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.1061+1G>C single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000721978] Chr1:119755426 [GRCh38]
Chr1:120298049 [GRCh37]
Chr1:1p12
likely pathogenic
NM_001166107.1(HMGCS2):c.71C>T (p.Thr24Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000706394] Chr1:119768774 [GRCh38]
Chr1:120311397 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.768G>A (p.Met256Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000691803] Chr1:119757395 [GRCh38]
Chr1:120300018 [GRCh37]
Chr1:1p12
uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12
likely benign
NM_001166107.1(HMGCS2):c.560-634C>T single nucleotide variant not provided [RCV000756248] Chr1:119759916 [GRCh38]
Chr1:120302539 [GRCh37]
Chr1:1p12
likely benign
NM_005518.4(HMGCS2):c.21A>G (p.Pro7=) single nucleotide variant not provided [RCV000977093] Chr1:119768824 [GRCh38]
Chr1:120311447 [GRCh37]
Chr1:1p12
likely benign
NM_005518.4(HMGCS2):c.880G>A (p.Asp294Asn) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001040515] Chr1:119757409 [GRCh38]
Chr1:120300032 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.502G>A (p.Gly168Ser) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001041480] Chr1:119764229 [GRCh38]
Chr1:120306852 [GRCh37]
Chr1:1p12
uncertain significance
NC_000001.11:g.(?_119768721)_(119768864_?)del deletion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001032719] Chr1:120311344..120311487 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.50C>T (p.Ala17Val) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001054365] Chr1:119768795 [GRCh38]
Chr1:120311418 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.664C>T (p.Arg222Trp) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000820917] Chr1:119759178 [GRCh38]
Chr1:120301801 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.891-316A>T single nucleotide variant not provided [RCV000831334] Chr1:119755913 [GRCh38]
Chr1:120298536 [GRCh37]
Chr1:1p12
likely benign
NM_001166107.1(HMGCS2):c.8G>A (p.Arg3His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000815725] Chr1:119768837 [GRCh38]
Chr1:120311460 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.560-514T>C single nucleotide variant not provided [RCV000835682] Chr1:119759796 [GRCh38]
Chr1:120302419 [GRCh37]
Chr1:1p12
benign
NM_001166107.1(HMGCS2):c.724+2T>C single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000797984] Chr1:119759116 [GRCh38]
Chr1:120301739 [GRCh37]
Chr1:1p12
pathogenic
NM_001166107.1(HMGCS2):c.1163C>T (p.Ala388Val) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000820039] Chr1:119753285 [GRCh38]
Chr1:120295908 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.724+309T>C single nucleotide variant not provided [RCV000831207] Chr1:119758809 [GRCh38]
Chr1:120301432 [GRCh37]
Chr1:1p12
benign
NM_001166107.1(HMGCS2):c.569G>T (p.Gly190Val) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000812481] Chr1:119759273 [GRCh38]
Chr1:120301896 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.617C>T (p.Ser206Leu) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000819843] Chr1:119759225 [GRCh38]
Chr1:120301848 [GRCh37]
Chr1:1p12
uncertain significance
NC_000001.11:g.(?_119768741)_(119768844_?)del deletion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000805922] Chr1:119768741..119768844 [GRCh38]
Chr1:120311364..120311467 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.791G>A (p.Arg264Gln) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001097610] Chr1:119759177 [GRCh38]
Chr1:120301800 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.803G>A (p.Arg268Gln) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001097609] Chr1:119759165 [GRCh38]
Chr1:120301788 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.1090T>A (p.Phe364Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001065916] Chr1:119755524 [GRCh38]
Chr1:120298147 [GRCh37]
Chr1:1p12
likely pathogenic|uncertain significance
NM_005518.4(HMGCS2):c.1017-302_1017-299del deletion not provided [RCV000831335] Chr1:119755896..119755899 [GRCh38]
Chr1:120298519..120298522 [GRCh37]
Chr1:1p12
benign
NM_001166107.1(HMGCS2):c.104G>T (p.Arg35Met) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000799471] Chr1:119768741 [GRCh38]
Chr1:120311364 [GRCh37]
Chr1:1p12
uncertain significance
NM_001166107.1(HMGCS2):c.105-266G>C single nucleotide variant not provided [RCV000844380] Chr1:119764892 [GRCh38]
Chr1:120307515 [GRCh37]
Chr1:1p12
benign
NM_001166107.1(HMGCS2):c.1295-217A>C single nucleotide variant not provided [RCV000844389] Chr1:119751125 [GRCh38]
Chr1:120293748 [GRCh37]
Chr1:1p12
benign
NM_005518.4(HMGCS2):c.1325C>T (p.Thr442Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001095815] Chr1:119752644 [GRCh38]
Chr1:120295267 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.*765G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099264] Chr1:119748082 [GRCh38]
Chr1:120290705 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.559+15G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099371] Chr1:119764157 [GRCh38]
Chr1:120306780 [GRCh37]
Chr1:1p12
uncertain significance
GRCh37/hg19 1p12(chr1:119425395-120527495)x3 copy number gain not provided [RCV000847309] Chr1:119425395..120527495 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.830T>A (p.Ile277Asn) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001097608] Chr1:119759138 [GRCh38]
Chr1:120301761 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.181_182insCCAATATGGCCCTGGAGGCCAA (p.Val61fs) insertion mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001170041] Chr1:119764549..119764550 [GRCh38]
Chr1:120307172..120307173 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.559+1G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001065915] Chr1:119764171 [GRCh38]
Chr1:120306794 [GRCh37]
Chr1:1p12
pathogenic|likely pathogenic
NM_005518.4(HMGCS2):c.1262T>G (p.Phe421Cys) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001234326] Chr1:119753312 [GRCh38]
Chr1:120295935 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.814T>C (p.Ser272Pro) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001227010] Chr1:119759154 [GRCh38]
Chr1:120301777 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.412T>C (p.Ser138Pro) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001221290] Chr1:119764319 [GRCh38]
Chr1:120306942 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.1132A>C (p.Asn378His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001095816] Chr1:119755482 [GRCh38]
Chr1:120298105 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.940C>T (p.Arg314Cys) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001095817] Chr1:119757349 [GRCh38]
Chr1:120299972 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.1161C>T (p.Tyr387=) single nucleotide variant not provided [RCV000979099] Chr1:119755453 [GRCh38]
Chr1:120298076 [GRCh37]
Chr1:1p12
likely benign
NM_005518.4(HMGCS2):c.111T>C (p.Ser37=) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV000885295] Chr1:119764620 [GRCh38]
Chr1:120307243 [GRCh37]
Chr1:1p12
benign|conflicting interpretations of pathogenicity
NM_005518.4(HMGCS2):c.1065A>G (p.Ala355=) single nucleotide variant not provided [RCV000937332] Chr1:119755549 [GRCh38]
Chr1:120298172 [GRCh37]
Chr1:1p12
likely benign
NM_005518.4(HMGCS2):c.1095C>G (p.Asp365Glu) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001238959] Chr1:119755519 [GRCh38]
Chr1:120298142 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.560-3C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001219076] Chr1:119759992 [GRCh38]
Chr1:120302615 [GRCh37]
Chr1:1p12
uncertain significance
NC_000001.11:g.119747985C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099261] Chr1:119747985 [GRCh38]
Chr1:120290608 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.1187+7A>T single nucleotide variant not provided [RCV000934375] Chr1:119755420 [GRCh38]
Chr1:120298043 [GRCh37]
Chr1:1p12
likely benign
NM_005518.4(HMGCS2):c.905C>T (p.Thr302Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001090000] Chr1:119757384 [GRCh38]
Chr1:120300007 [GRCh37]
Chr1:1p12
likely pathogenic
NM_005518.4(HMGCS2):c.*155C>T single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001101261] Chr1:119748692 [GRCh38]
Chr1:120291315 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.*139C>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001101262] Chr1:119748708 [GRCh38]
Chr1:120291331 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.*822G>A single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001099262] Chr1:119748025 [GRCh38]
Chr1:120290648 [GRCh37]
Chr1:1p12
benign
NM_005518.4(HMGCS2):c.704T>C (p.Met235Thr) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001097611] Chr1:119759264 [GRCh38]
Chr1:120301887 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.146C>T (p.Thr49Ile) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001232384] Chr1:119764585 [GRCh38]
Chr1:120307208 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.428C>G (p.Thr143Arg) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001235292] Chr1:119764303 [GRCh38]
Chr1:120306926 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.*12A>C single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001101263] Chr1:119748835 [GRCh38]
Chr1:120291458 [GRCh37]
Chr1:1p12
benign
NM_005518.4(HMGCS2):c.1082A>G (p.Gln361Arg) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001228982] Chr1:119755532 [GRCh38]
Chr1:120298155 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.533A>G (p.Asn178Ser) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001064667] Chr1:119764198 [GRCh38]
Chr1:120306821 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.512C>T (p.Ala171Val) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001089999] Chr1:119764219 [GRCh38]
Chr1:120306842 [GRCh37]
Chr1:1p12
likely pathogenic
NM_005518.4(HMGCS2):c.1480C>T (p.Arg494Ter) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001255221] Chr1:119750849 [GRCh38]
Chr1:120293472 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.103A>G (p.Arg35Gly) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001299698] Chr1:119768742 [GRCh38]
Chr1:120311365 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.682C>T (p.Arg228Ter) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001330065] Chr1:119759867 [GRCh38]
Chr1:120302490 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.245G>A (p.Gly82Glu) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001326908] Chr1:119764486 [GRCh38]
Chr1:120307109 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.586G>C (p.Asp196His) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001315300] Chr1:119759963 [GRCh38]
Chr1:120302586 [GRCh37]
Chr1:1p12
uncertain significance
NM_005518.4(HMGCS2):c.726C>G (p.Tyr242Ter) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001330066] Chr1:119759242 [GRCh38]
Chr1:120301865 [GRCh37]
Chr1:1p12
pathogenic
NM_005518.4(HMGCS2):c.810C>G (p.Tyr270Ter) single nucleotide variant mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency [RCV001336824] Chr1:119759158 [GRCh38]
Chr1:120301781 [GRCh37]
Chr1:1p12
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5008 AgrOrtholog
COSMIC HMGCS2 COSMIC
Ensembl Genes ENSG00000134240 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000358414 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000439495 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000369406 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000544913 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.47.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000134240 GTEx
HGNC ID HGNC:5008 ENTREZGENE
Human Proteome Map HMGCS2 Human Proteome Map
InterPro HMG_CoA_synt_AS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_CoA_synt_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_CoA_synth_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_CoA_synthase_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thiolase-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:3158 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 3158 ENTREZGENE
OMIM 600234 OMIM
  605911 OMIM
Pfam HMG_CoA_synt_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_CoA_synt_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29338 PharmGKB
PROSITE HMG_COA_SYNTHASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53901 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs HMG-CoA-S_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A140VJL2 ENTREZGENE, UniProtKB/TrEMBL
  HMCS2_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B7Z8R3 UniProtKB/Swiss-Prot
  D3Y5K6 UniProtKB/Swiss-Prot
  Q5SZU2 UniProtKB/Swiss-Prot
  Q6IBF4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-26 HMGCS2  3-hydroxy-3-methylglutaryl-CoA synthase 2    3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  Symbol and/or name change 5135510 APPROVED
2011-08-17 HMGCS2  3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  HMGCS2  3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  Symbol and/or name change 5135510 APPROVED
2011-07-27 HMGCS2  3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)  HMGCS2  3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)  Symbol and/or name change 5135510 APPROVED