BHMT (betaine--homocysteine S-methyltransferase) - Rat Genome Database

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Gene: BHMT (betaine--homocysteine S-methyltransferase) Homo sapiens
Analyze
Symbol: BHMT
Name: betaine--homocysteine S-methyltransferase
RGD ID: 1346951
HGNC Page HGNC:1047
Description: Enables betaine-homocysteine S-methyltransferase activity and zinc ion binding activity. Involved in 'de novo' L-methionine biosynthetic process; L-methionine salvage; and amino-acid betaine metabolic process. Located in extracellular exosome. Implicated in cerebral infarction and pulmonary embolism. Biomarker of hepatocellular carcinoma.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: betaine homocysteine methyltransferase; betaine--homocysteine S-methyltransferase 1; betaine-homocysteine methyltransferase; BHMT1; epididymis secretory sperm binding protein Li 61p; HEL-S-61p
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38579,111,809 - 79,132,288 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl579,111,809 - 79,132,288 (+)EnsemblGRCh38hg38GRCh38
GRCh37578,407,632 - 78,428,111 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36578,443,360 - 78,463,869 (+)NCBINCBI36Build 36hg18NCBI36
Build 34578,443,438 - 78,463,863NCBI
Celera574,300,507 - 74,323,326 (+)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef573,613,559 - 73,636,443 (+)NCBIHuRef
CHM1_1577,840,080 - 77,860,596 (+)NCBICHM1_1
T2T-CHM13v2.0579,592,579 - 79,615,902 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+/-)-Aegeline  (ISO)
(1->4)-beta-D-glucan  (ISO)
(RS)-coclaurine  (ISO)
(RS)-norcoclaurine  (ISO)
(S)-coclaurine  (ISO)
1,2-dichloroethane  (ISO)
1-(3-(trifluoromethyl)phenyl)piperazine  (ISO)
1-benzylpiperazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-tribromophenol  (EXP)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2,4-dinitrotoluene  (ISO)
2,6-dinitrotoluene  (ISO)
2-nitrofluorene  (ISO)
3,3',5,5'-tetrabromobisphenol A  (EXP)
3-chloropropane-1,2-diol  (ISO)
3H-1,2-dithiole-3-thione  (ISO)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (ISO)
6-propyl-2-thiouracil  (ISO)
acrylamide  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (EXP)
amiodarone  (ISO)
amitriptyline  (ISO)
amitrole  (ISO)
ammonium chloride  (ISO)
andrographolide  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (EXP)
azoxystrobin  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (ISO)
beta-naphthoflavone  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bromobenzene  (ISO)
buta-1,3-diene  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
CGP 52608  (EXP)
chlorpyrifos  (ISO)
choline  (ISO)
ciglitazone  (EXP)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clomipramine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (EXP)
corn oil  (ISO)
coumarin  (ISO)
Cuprizon  (ISO)
cyclosporin A  (EXP)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
diethyl maleate  (ISO)
diethylstilbestrol  (ISO)
diquat  (ISO)
dorsomorphin  (EXP)
endosulfan  (ISO)
epoxiconazole  (ISO)
ethanol  (ISO)
fenthion  (ISO)
fentin chloride  (ISO)
folic acid  (ISO)
fructose  (ISO)
fumonisin B1  (ISO)
furan  (ISO)
glafenine  (ISO)
glucose  (ISO)
glycine betaine  (EXP)
glyphosate  (ISO)
imidacloprid  (ISO)
imipramine  (ISO)
iodide salt  (ISO)
ketoconazole  (ISO)
L-methionine  (EXP,ISO)
lead diacetate  (ISO)
mercury dichloride  (ISO)
methapyrilene  (ISO)
methidathion  (ISO)
methimazole  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
N-nitrosodiethylamine  (ISO)
N-nitrosodimethylamine  (ISO)
N-nitrosomorpholine  (ISO)
nefazodone  (ISO)
nimesulide  (ISO)
nitrofen  (ISO)
O-methyleugenol  (EXP)
ochratoxin A  (ISO)
paracetamol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phorbol 13-acetate 12-myristate  (ISO)
piperonyl butoxide  (ISO)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
quercetin  (EXP,ISO)
resveratrol  (ISO)
SB 431542  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
streptozocin  (ISO)
sulfadimethoxine  (ISO)
sunitinib  (EXP)
tert-butyl hydroperoxide  (EXP)
tetrachloromethane  (ISO)
thiabendazole  (ISO)
thioacetamide  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
trichloroethene  (ISO)
trichostatin A  (EXP)
triphenyl phosphate  (ISO)
tris(2-butoxyethyl) phosphate  (EXP)
urethane  (EXP)
valdecoxib  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
vinclozolin  (ISO)
yohimbine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Overview of homocysteine and folate metabolism. With special references to cardiovascular disease and neural tube defects. Blom HJ and Smulders Y, J Inherit Metab Dis. 2011 Feb;34(1):75-81. doi: 10.1007/s10545-010-9177-4. Epub 2010 Sep 4.
2. Significant Down-Regulation of Urea Cycle Generates Clinically Relevant Proteomic Signature in Hepatocellular Carcinoma Patients with Macrovascular Invasion. Cao Y, etal., J Proteome Res. 2019 May 3;18(5):2032-2044. doi: 10.1021/acs.jproteome.8b00921. Epub 2019 Mar 29.
3. Early-onset ischaemic stroke: analysis of 58 polymorphisms in 17 genes involved in methionine metabolism. Giusti B, etal., Thromb Haemost. 2010 Aug;104(2):231-42. doi: 10.1160/TH09-11-0748. Epub 2010 May 10.
4. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
5. The clinical significance of betaine, an osmolyte with a key role in methyl group metabolism. Lever M and Slow S, Clin Biochem. 2010 Jun;43(9):732-44. doi: 10.1016/j.clinbiochem.2010.03.009. Epub 2010 Mar 25.
6. S-adenosylmethionine in liver health, injury, and cancer. Lu SC and Mato JM, Physiol Rev. 2012 Oct;92(4):1515-42. doi: 10.1152/physrev.00047.2011.
7. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
8. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. BHMT polymorphism and susceptibility to PTE in Chinese patients. Zhang WH, etal., Eur Rev Med Pharmacol Sci. 2023 May;27(9):4098-4102. doi: 10.26355/eurrev_202305_32317.
Additional References at PubMed
PMID:1657504   PMID:8798461   PMID:8889548   PMID:9281325   PMID:9681996   PMID:10075673   PMID:10529246   PMID:11223523   PMID:11516176   PMID:11883905   PMID:12071701   PMID:12220488  
PMID:12475213   PMID:12477932   PMID:12749058   PMID:12818402   PMID:15122900   PMID:15489334   PMID:16189514   PMID:16344560   PMID:16816108   PMID:16953798   PMID:17035141   PMID:17119116  
PMID:17376725   PMID:17436311   PMID:17705221   PMID:17993766   PMID:18000879   PMID:18029348   PMID:18230605   PMID:18230680   PMID:18262489   PMID:18427977   PMID:18457970   PMID:18498552  
PMID:18635682   PMID:18676680   PMID:18708404   PMID:18830263   PMID:18988749   PMID:19048631   PMID:19161160   PMID:19170196   PMID:19336437   PMID:19493349   PMID:19625176   PMID:19635752  
PMID:19683694   PMID:19692168   PMID:19737740   PMID:19777601   PMID:19913121   PMID:19936946   PMID:19948975   PMID:20031554   PMID:20346360   PMID:20453000   PMID:20628086   PMID:20634891  
PMID:20662904   PMID:20664391   PMID:20737570   PMID:21082674   PMID:21093336   PMID:21349258   PMID:21564312   PMID:21565678   PMID:21630102   PMID:21873635   PMID:21988832   PMID:22138536  
PMID:22339686   PMID:22339736   PMID:23241634   PMID:23376485   PMID:23378610   PMID:23533145   PMID:23645037   PMID:23720494   PMID:24816252   PMID:24895213   PMID:25144858   PMID:25343990  
PMID:25416956   PMID:25846410   PMID:26186194   PMID:26213999   PMID:26592251   PMID:27677362   PMID:27735840   PMID:28514442   PMID:28582843   PMID:29356306   PMID:29407547   PMID:31044529  
PMID:31451344   PMID:31558761   PMID:32235678   PMID:33894044   PMID:33961781   PMID:33975330   PMID:39117631  


Genomics

Comparative Map Data
BHMT
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38579,111,809 - 79,132,288 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl579,111,809 - 79,132,288 (+)EnsemblGRCh38hg38GRCh38
GRCh37578,407,632 - 78,428,111 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36578,443,360 - 78,463,869 (+)NCBINCBI36Build 36hg18NCBI36
Build 34578,443,438 - 78,463,863NCBI
Celera574,300,507 - 74,323,326 (+)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef573,613,559 - 73,636,443 (+)NCBIHuRef
CHM1_1577,840,080 - 77,860,596 (+)NCBICHM1_1
T2T-CHM13v2.0579,592,579 - 79,615,902 (+)NCBIT2T-CHM13v2.0
Bhmt
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391393,753,399 - 93,774,266 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1393,753,183 - 93,774,469 (-)EnsemblGRCm39 Ensembl
GRCm381393,616,891 - 93,637,758 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1393,616,675 - 93,637,961 (-)EnsemblGRCm38mm10GRCm38
MGSCv371394,386,846 - 94,407,713 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361394,717,644 - 94,738,511 (-)NCBIMGSCv36mm8
Celera1397,222,393 - 97,243,812 (-)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1347.87NCBI
Bhmt
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8226,594,852 - 26,614,429 (-)NCBIGRCr8
mRatBN7.2224,859,871 - 24,879,449 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl224,859,873 - 24,879,742 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx231,887,170 - 31,906,744 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0229,987,440 - 30,007,012 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0224,813,713 - 24,832,877 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0223,236,573 - 23,256,158 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl223,236,575 - 23,256,158 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0242,417,998 - 42,437,775 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4223,923,651 - 23,943,320 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1223,844,021 - 23,863,689 (-)NCBI
Celera220,935,059 - 20,954,426 (-)NCBICelera
Cytogenetic Map2q12NCBI
Bhmt
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542521,991,665 - 22,009,855 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542521,992,219 - 22,009,389 (-)NCBIChiLan1.0ChiLan1.0
BHMT
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2436,174,948 - 36,195,674 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1534,328,575 - 34,351,766 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0536,181,183 - 36,201,833 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1536,670,854 - 36,691,942 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl536,670,854 - 36,728,993 (-)Ensemblpanpan1.1panPan2
BHMT
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1327,732,381 - 27,752,168 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl327,734,108 - 27,752,046 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha328,973,220 - 28,991,599 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0327,652,772 - 27,671,416 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl327,651,360 - 27,671,308 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1327,591,867 - 27,610,507 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0327,570,180 - 27,588,856 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0327,851,113 - 27,869,743 (-)NCBIUU_Cfam_GSD_1.0
LOC101972215
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213183,901,611 - 183,920,782 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365496,938,092 - 6,957,363 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365496,938,100 - 6,956,380 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
BHMT
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl287,910,603 - 87,935,252 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1287,911,093 - 87,935,252 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2289,406,703 - 89,431,091 (-)NCBISscrofa10.2Sscrofa10.2susScr3
BHMT
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1473,331,551 - 73,352,259 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl473,332,259 - 73,352,434 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604922,178,695 - 22,198,656 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Bhmt
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248693,617,948 - 3,642,860 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248693,618,895 - 3,639,621 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in BHMT
34 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5q13.3-22.1(chr5:74163186-110809453)x3 copy number gain See cases [RCV000051839] Chr5:74163186..110809453 [GRCh38]
Chr5:73459011..110145153 [GRCh37]
Chr5:73494767..110173052 [NCBI36]
Chr5:5q13.3-22.1
pathogenic
GRCh38/hg38 5q14.1(chr5:78804361-79620179)x3 copy number gain See cases [RCV000138660] Chr5:78804361..79620179 [GRCh38]
Chr5:78100184..78916002 [GRCh37]
Chr5:78135940..78951758 [NCBI36]
Chr5:5q14.1
uncertain significance
GRCh38/hg38 5q14.1(chr5:79028408-79195058)x3 copy number gain See cases [RCV000140959] Chr5:79028408..79195058 [GRCh38]
Chr5:78324231..78490881 [GRCh37]
Chr5:78359987..78526637 [NCBI36]
Chr5:5q14.1
likely benign
NM_001713.3(BHMT):c.1200del (p.Lys400fs) deletion not provided [RCV000190384] Chr5:79131091 [GRCh38]
Chr5:78426914 [GRCh37]
Chr5:5q14.1
not provided
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_001713.3(BHMT):c.628G>A (p.Ala210Thr) single nucleotide variant not specified [RCV004311334] Chr5:79126048 [GRCh38]
Chr5:78421871 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5q14.1(chr5:78265041-78558425)x3 copy number gain not provided [RCV000744878] Chr5:78265041..78558425 [GRCh37]
Chr5:5q14.1
benign
GRCh37/hg19 5q14.1(chr5:78397980-78427208)x3 copy number gain not provided [RCV000744884] Chr5:78397980..78427208 [GRCh37]
Chr5:5q14.1
benign
GRCh37/hg19 5q14.1(chr5:78397980-78436211)x3 copy number gain not provided [RCV000744885] Chr5:78397980..78436211 [GRCh37]
Chr5:5q14.1
benign
NM_001713.3(BHMT):c.222C>T (p.Phe74=) single nucleotide variant not provided [RCV000883761] Chr5:79119314 [GRCh38]
Chr5:78415137 [GRCh37]
Chr5:5q14.1
benign
NM_001713.3(BHMT):c.589C>T (p.Pro197Ser) single nucleotide variant not provided [RCV000883762] Chr5:79121329 [GRCh38]
Chr5:78417152 [GRCh37]
Chr5:5q14.1
benign
Single allele deletion Neurodevelopmental disorder [RCV000787436] Chr5:14685137..149511942 [GRCh37]
Chr5:5p15.2-q32
uncertain significance
GRCh37/hg19 5q14.1(chr5:78318239-78791047)x3 copy number gain not provided [RCV000849615] Chr5:78318239..78791047 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78323433-78693915)x3 copy number gain not provided [RCV000847079] Chr5:78323433..78693915 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78324437-78693659)x3 copy number gain not provided [RCV000847157] Chr5:78324437..78693659 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78366704-78651243)x3 copy number gain not provided [RCV001005688] Chr5:78366704..78651243 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78229182-78844914)x3 copy number gain not provided [RCV000847383] Chr5:78229182..78844914 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78094810-78936391)x3 copy number gain not provided [RCV001005686] Chr5:78094810..78936391 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78401788-78708407)x3 copy number gain not provided [RCV001005689] Chr5:78401788..78708407 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78323433-78693915)x3 copy number gain not provided [RCV000846882] Chr5:78323433..78693915 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.19A>C (p.Lys7Gln) single nucleotide variant not specified [RCV004305123] Chr5:79111904 [GRCh38]
Chr5:78407727 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.121G>C (p.Ala41Pro) single nucleotide variant not specified [RCV004300906] Chr5:79115854 [GRCh38]
Chr5:78411677 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.595G>A (p.Gly199Ser) single nucleotide variant not provided [RCV000954255] Chr5:79121335 [GRCh38]
Chr5:78417158 [GRCh37]
Chr5:5q14.1
benign
GRCh37/hg19 5q13.2-15(chr5:72790061-97478870)x3 copy number gain not provided [RCV001005683] Chr5:72790061..97478870 [GRCh37]
Chr5:5q13.2-15
pathogenic
GRCh37/hg19 5q14.1(chr5:78366704-78689771)x3 copy number gain not provided [RCV001005687] Chr5:78366704..78689771 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78406853-78524612)x1 copy number loss not provided [RCV001834265] Chr5:78406853..78524612 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78196511-78445636)x1 copy number loss not provided [RCV001827688] Chr5:78196511..78445636 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:78364368-78591431)x3 copy number gain not provided [RCV001834180] Chr5:78364368..78591431 [GRCh37]
Chr5:5q14.1
uncertain significance
GRCh37/hg19 5q14.1(chr5:77746948-79089197)x1 copy number loss not provided [RCV002474865] Chr5:77746948..79089197 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.748G>T (p.Ala250Ser) single nucleotide variant not specified [RCV004111075] Chr5:79126168 [GRCh38]
Chr5:78421991 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.182G>A (p.Arg61Gln) single nucleotide variant not specified [RCV004213889] Chr5:79119274 [GRCh38]
Chr5:78415097 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.212T>A (p.Met71Lys) single nucleotide variant not specified [RCV004100486] Chr5:79119304 [GRCh38]
Chr5:78415127 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.184G>C (p.Glu62Gln) single nucleotide variant not specified [RCV004108545] Chr5:79119276 [GRCh38]
Chr5:78415099 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.1141G>A (p.Glu381Lys) single nucleotide variant not specified [RCV004213788] Chr5:79131036 [GRCh38]
Chr5:78426859 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.887T>C (p.Ile296Thr) single nucleotide variant not specified [RCV004225613] Chr5:79127833 [GRCh38]
Chr5:78423656 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.169C>T (p.Arg57Cys) single nucleotide variant not specified [RCV004230564] Chr5:79119261 [GRCh38]
Chr5:78415084 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.610C>T (p.Arg204Cys) single nucleotide variant not specified [RCV004090450] Chr5:79121350 [GRCh38]
Chr5:78417173 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.160G>A (p.Glu54Lys) single nucleotide variant not specified [RCV004092792] Chr5:79115893 [GRCh38]
Chr5:78411716 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.616G>C (p.Val206Leu) single nucleotide variant not specified [RCV004089921] Chr5:79121356 [GRCh38]
Chr5:78417179 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.352G>A (p.Val118Ile) single nucleotide variant not specified [RCV004233033] Chr5:79120416 [GRCh38]
Chr5:78416239 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.809G>A (p.Gly270Glu) single nucleotide variant not specified [RCV004248024] Chr5:79127755 [GRCh38]
Chr5:78423578 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.170G>T (p.Arg57Leu) single nucleotide variant not specified [RCV004336480] Chr5:79119262 [GRCh38]
Chr5:78415085 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.487C>T (p.His163Tyr) single nucleotide variant not specified [RCV004357535] Chr5:79121227 [GRCh38]
Chr5:78417050 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.112T>A (p.Tyr38Asn) single nucleotide variant not specified [RCV004360215] Chr5:79115845 [GRCh38]
Chr5:78411668 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.857G>A (p.Arg286Lys) single nucleotide variant not specified [RCV004349924] Chr5:79127803 [GRCh38]
Chr5:78423626 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.767G>A (p.Cys256Tyr) single nucleotide variant BHMT-related disorder [RCV003913849] Chr5:79126187 [GRCh38]
Chr5:78422010 [GRCh37]
Chr5:5q14.1
likely benign
NM_001713.3(BHMT):c.700G>T (p.Gly234Cys) single nucleotide variant not specified [RCV004429113] Chr5:79126120 [GRCh38]
Chr5:78421943 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.115G>A (p.Val39Ile) single nucleotide variant not specified [RCV004429110] Chr5:79115848 [GRCh38]
Chr5:78411671 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.649T>G (p.Cys217Gly) single nucleotide variant not specified [RCV004429112] Chr5:79126069 [GRCh38]
Chr5:78421892 [GRCh37]
Chr5:5q14.1
uncertain significance
NM_001713.3(BHMT):c.397A>G (p.Ser133Gly) single nucleotide variant not specified [RCV004607035] Chr5:79120461 [GRCh38]
Chr5:78416284 [GRCh37]
Chr5:5q14.1
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1143
Count of miRNA genes:720
Interacting mature miRNAs:812
Transcripts:ENST00000274353, ENST00000520335, ENST00000520703, ENST00000521279, ENST00000523508, ENST00000524080
Prediction methods:Microtar, Miranda, Rnahybrid
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407148294GWAS797270_Hselenium measurement QTL GWAS797270 (human)6e-11selenium measurement57912936579129366Human
407406732GWAS1055708_Hhigh density lipoprotein cholesterol measurement QTL GWAS1055708 (human)2e-09high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)57912613679126137Human
407281603GWAS930579_Hbody height QTL GWAS930579 (human)3e-09body height (VT:0001253)body height (CMO:0000106)57911851479118515Human
407098758GWAS747734_Hplasma betaine measurement QTL GWAS747734 (human)1e-28plasma betaine measurement57913082779130828Human
407419694GWAS1068670_HC-reactive protein measurement QTL GWAS1068670 (human)2e-11C-reactive protein measurementblood C-reactive protein level (CMO:0003160)57912180679121807Human
407224687GWAS873663_Hselenium measurement QTL GWAS873663 (human)8e-20selenium measurement57912059379120594Human
407224681GWAS873657_Hselenium measurement QTL GWAS873657 (human)2e-11selenium measurement57911550179115502Human
407224683GWAS873659_Hselenium measurement QTL GWAS873659 (human)0.000005selenium measurement57912059379120594Human
407005293GWAS654269_Hserum selenium measurement QTL GWAS654269 (human)8e-12serum selenium measurement57911851479118515Human
407252918GWAS901894_Hhigh density lipoprotein cholesterol measurement QTL GWAS901894 (human)2e-08high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)57912213379122134Human
407390043GWAS1039019_Hserum gamma-glutamyl transferase measurement QTL GWAS1039019 (human)8e-12serum gamma-glutamyl transferase measurementserum gamma-glutamyltransferase activity level (CMO:0002241)57912398679123987Human
407058519GWAS707495_Hhigh density lipoprotein cholesterol measurement QTL GWAS707495 (human)4e-11high density lipoprotein cholesterol measurementblood high density lipoprotein cholesterol level (CMO:0000052)57912613679126137Human
407219731GWAS868707_Hserum metabolite measurement QTL GWAS868707 (human)7e-15serum metabolite measurement57912833179128332Human
407249489GWAS898465_Hserum gamma-glutamyl transferase measurement QTL GWAS898465 (human)2e-10serum gamma-glutamyl transferase measurementserum gamma-glutamyltransferase activity level (CMO:0002241)57912490979124910Human

Markers in Region
RH16250  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,426,866 - 78,427,013UniSTSGRCh37
Build 36578,462,622 - 78,462,769RGDNCBI36
Celera574,319,764 - 74,319,911RGD
Celera574,322,079 - 74,322,226UniSTS
Cytogenetic Map5q14.1UniSTS
HuRef573,635,196 - 73,635,343UniSTS
GeneMap99-GB4 RH Map5374.74UniSTS
NCBI RH Map5386.0UniSTS
RH35961  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,427,197 - 78,427,344UniSTSGRCh37
Build 36578,462,953 - 78,463,100RGDNCBI36
Celera574,322,410 - 74,322,557RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,635,527 - 73,635,674UniSTS
GeneMap99-GB4 RH Map5373.94UniSTS
NCBI RH Map5368.4UniSTS
SGC33609  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,427,299 - 78,427,448UniSTSGRCh37
Build 36578,463,055 - 78,463,204RGDNCBI36
Celera574,322,512 - 74,322,661RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,635,629 - 73,635,778UniSTS
GeneMap99-GB4 RH Map5373.69UniSTS
Whitehead-RH Map5274.2UniSTS
NCBI RH Map5396.8UniSTS
RH91498  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,427,765 - 78,427,898UniSTSGRCh37
Build 36578,463,521 - 78,463,654RGDNCBI36
Celera574,322,978 - 74,323,111RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,636,095 - 73,636,228UniSTS
GeneMap99-GB4 RH Map5373.61UniSTS
RH80672  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,423,787 - 78,424,013UniSTSGRCh37
Build 36578,459,543 - 78,459,769RGDNCBI36
Celera574,316,682 - 74,316,908RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,629,636 - 73,629,862UniSTS
GeneMap99-GB4 RH Map5376.27UniSTS
SHGC-33971  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,410,997 - 78,411,121UniSTSGRCh37
Build 36578,446,753 - 78,446,877RGDNCBI36
Celera574,303,900 - 74,304,024RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,616,952 - 73,617,076UniSTS
TNG Radiation Hybrid Map536789.0UniSTS
Stanford-G3 RH Map52916.0UniSTS
GeneMap99-G3 RH Map52911.0UniSTS
SHGC-56646  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,413,286 - 78,413,584UniSTSGRCh37
Build 36578,449,042 - 78,449,340RGDNCBI36
Celera574,306,186 - 74,306,484RGD
Cytogenetic Map5q14.1UniSTS
HuRef573,619,238 - 73,619,536UniSTS
TNG Radiation Hybrid Map536797.0UniSTS
BHMT_54.2  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37578,427,391 - 78,428,259UniSTSGRCh37
Build 36578,463,147 - 78,464,015RGDNCBI36
Celera574,322,604 - 74,323,472RGD
HuRef573,635,721 - 73,636,589UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
1201 2289 2645 2155 4668 1704 2149 610 1006 455 2131 6035 5428 9 3560 811 1602 1435 162

Sequence


Ensembl Acc Id: ENST00000274353   ⟹   ENSP00000274353
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,111,809 - 79,132,288 (+)Ensembl
Ensembl Acc Id: ENST00000520335
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,111,809 - 79,116,404 (+)Ensembl
Ensembl Acc Id: ENST00000520703
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,111,809 - 79,119,606 (+)Ensembl
Ensembl Acc Id: ENST00000521279
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,121,281 - 79,128,197 (+)Ensembl
Ensembl Acc Id: ENST00000523508
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,120,352 - 79,126,297 (+)Ensembl
Ensembl Acc Id: ENST00000524080   ⟹   ENSP00000428240
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl579,111,809 - 79,131,484 (+)Ensembl
RefSeq Acc Id: NM_001713   ⟹   NP_001704
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38579,111,809 - 79,132,288 (+)NCBI
GRCh37578,407,604 - 78,428,113 (+)ENTREZGENE
Build 36578,443,360 - 78,463,869 (+)NCBI Archive
HuRef573,613,559 - 73,636,443 (+)ENTREZGENE
CHM1_1577,840,080 - 77,860,596 (+)NCBI
T2T-CHM13v2.0579,592,914 - 79,615,902 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054353042   ⟹   XP_054209017
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0579,592,579 - 79,615,902 (+)NCBI
RefSeq Acc Id: NP_001704   ⟸   NM_001713
- UniProtKB: Q9UNI9 (UniProtKB/Swiss-Prot),   Q93088 (UniProtKB/Swiss-Prot),   V9HWA4 (UniProtKB/TrEMBL),   B2RCQ6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000274353   ⟸   ENST00000274353
Ensembl Acc Id: ENSP00000428240   ⟸   ENST00000524080
RefSeq Acc Id: XP_054209017   ⟸   XM_054353042
- Peptide Label: isoform X1
Protein Domains
Hcy-binding

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q93088-F1-model_v2 AlphaFold Q93088 1-406 view protein structure

Promoters
RGD ID:6869978
Promoter ID:EPDNEW_H8154
Type:multiple initiation site
Name:BHMT_1
Description:betaine--homocysteine S-methyltransferase
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
GRCh38579,111,810 - 79,111,870EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:1047 AgrOrtholog
COSMIC BHMT COSMIC
Ensembl Genes ENSG00000145692 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000274353 ENTREZGENE
  ENST00000274353.10 UniProtKB/Swiss-Prot
  ENST00000524080.1 UniProtKB/TrEMBL
Gene3D-CATH 3.20.20.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000145692 GTEx
HGNC ID HGNC:1047 ENTREZGENE
Human Proteome Map BHMT Human Proteome Map
InterPro Betaine-hCys_S-MeTrfase_BHMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BHMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HCY_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:635 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 635 ENTREZGENE
OMIM 602888 OMIM
PANTHER BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1 UniProtKB/Swiss-Prot
  BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1 UniProtKB/Swiss-Prot
  BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1 UniProtKB/TrEMBL
  BETAINE--HOMOCYSTEINE S-METHYLTRANSFERASE 1 UniProtKB/TrEMBL
Pfam S-methyl_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA25350 PharmGKB
PIRSF Betaine_HMT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HCY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF82282 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt B2RCQ6 ENTREZGENE, UniProtKB/TrEMBL
  BHMT1_HUMAN UniProtKB/Swiss-Prot
  E5RJH0_HUMAN UniProtKB/TrEMBL
  Q93088 ENTREZGENE
  Q9UNI9 ENTREZGENE
  V9HWA4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q9UNI9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-07-27 BHMT  betaine--homocysteine S-methyltransferase  BHMT  betaine-homocysteine methyltransferase  Symbol and/or name change 5135510 APPROVED