HENMT1 (HEN methyltransferase 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: HENMT1 (HEN methyltransferase 1) Homo sapiens
Analyze
Symbol: HENMT1
Name: HEN methyltransferase 1
RGD ID: 1602307
HGNC Page HGNC:26400
Description: Enables small RNA 2'-O-methyltransferase activity. Involved in RNA methylation. Predicted to be located in P granule. Predicted to be active in cytoplasm and nucleus.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C1orf59; FLJ30525; HEN1; HEN1 methyltransferase homolog; HEN1 methyltransferase homolog 1; HEN1 methyltransferase homolog 1 (Arabidopsis); hua enhancer 1 homolog 1; hypothetical protein LOC113802; MGC111091; RP11-256E16.2; small RNA 2'-O-methyltransferase
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
GRCh381108,648,295 - 108,661,474 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1108,648,290 - 108,661,526 (-)EnsemblGRCh38hg38GRCh38
GRCh371109,190,917 - 109,204,096 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361108,992,433 - 109,005,671 (-)NCBINCBI36Build 36hg18NCBI36
Celera1107,460,828 - 107,474,037 (-)NCBICelera
Cytogenetic Map1p13.3NCBI
HuRef1107,083,630 - 107,096,727 (-)NCBIHuRef
CHM1_11109,305,731 - 109,318,961 (-)NCBICHM1_1
T2T-CHM13v2.01108,681,289 - 108,694,467 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IEA)
nucleus  (IBA)
P granule  (ISS)

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Autism  (IAGP)
Azoospermia  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11283698   PMID:12477932   PMID:14702039   PMID:15342556   PMID:17207965   PMID:21873635   PMID:22458338   PMID:25416956   PMID:26496356   PMID:28514442   PMID:28676534   PMID:29277012  
PMID:29703750   PMID:32296183   PMID:33961781   PMID:38065897  


Genomics

Comparative Map Data
HENMT1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381108,648,295 - 108,661,474 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1108,648,290 - 108,661,526 (-)EnsemblGRCh38hg38GRCh38
GRCh371109,190,917 - 109,204,096 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361108,992,433 - 109,005,671 (-)NCBINCBI36Build 36hg18NCBI36
Celera1107,460,828 - 107,474,037 (-)NCBICelera
Cytogenetic Map1p13.3NCBI
HuRef1107,083,630 - 107,096,727 (-)NCBIHuRef
CHM1_11109,305,731 - 109,318,961 (-)NCBICHM1_1
T2T-CHM13v2.01108,681,289 - 108,694,467 (-)NCBIT2T-CHM13v2.0
Henmt1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393108,846,770 - 108,887,201 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3108,847,375 - 108,868,090 (+)EnsemblGRCm39 Ensembl
GRCm383108,939,454 - 108,979,885 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3108,940,059 - 108,960,774 (+)EnsemblGRCm38mm10GRCm38
MGSCv373108,743,002 - 108,763,694 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363109,068,140 - 109,088,732 (+)NCBIMGSCv36mm8
Celera3111,275,307 - 111,295,934 (+)NCBICelera
Cytogenetic Map3F3NCBI
cM Map347.99NCBI
Henmt1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82199,258,107 - 199,291,739 (+)NCBIGRCr8
mRatBN7.22196,585,732 - 196,603,700 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2196,586,797 - 196,599,738 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2204,230,540 - 204,242,798 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02202,118,362 - 202,130,609 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02196,935,420 - 196,947,668 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02211,740,571 - 211,753,718 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02231,214,546 - 231,225,175 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42204,544,606 - 204,558,076 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12204,506,770 - 204,520,830 (+)NCBI
Celera2189,235,772 - 189,247,793 (+)NCBICelera
Cytogenetic Map2q41NCBI
Henmt1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543512,138,177 - 12,154,630 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543512,137,537 - 12,154,630 (-)NCBIChiLan1.0ChiLan1.0
HENMT1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21118,641,837 - 118,657,252 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11117,801,704 - 117,817,082 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01111,023,949 - 111,037,138 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11110,191,227 - 110,204,275 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1110,191,227 - 110,204,270 (-)Ensemblpanpan1.1panPan2
HENMT1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha645,928,483 - 45,943,590 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0643,396,229 - 43,435,695 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl643,428,453 - 43,435,709 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1643,152,578 - 43,167,498 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0643,084,944 - 43,088,221 (+)NCBIUNSW_CanFamBas_1.0
UNSW_CanFamBas_1.0643,125,908 - 43,140,909 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0643,552,275 - 43,567,220 (+)NCBIUU_Cfam_GSD_1.0
Henmt1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505819,857,460 - 19,870,919 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936704242,262 - 256,739 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HENMT1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4111,364,966 - 111,382,572 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14111,364,456 - 111,382,582 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24121,863,155 - 121,881,143 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HENMT1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12024,920,224 - 24,936,429 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2024,921,611 - 24,936,419 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603833,410,548 - 33,426,967 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Henmt1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247724,456,917 - 4,470,558 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247724,452,320 - 4,470,097 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in HENMT1
24 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p21.2-13.2(chr1:101618097-111703028)x1 copy number loss See cases [RCV000053879] Chr1:101618097..111703028 [GRCh38]
Chr1:102083653..112245650 [GRCh37]
Chr1:101856241..112047173 [NCBI36]
Chr1:1p21.2-13.2		 pathogenic
GRCh38/hg38 1p21.1-13.3(chr1:106074587-110144290)x1 copy number loss See cases [RCV000053881] Chr1:106074587..110144290 [GRCh38]
Chr1:106617209..110686912 [GRCh37]
Chr1:106418732..110488435 [NCBI36]
Chr1:1p21.1-13.3		 pathogenic
GRCh38/hg38 1p21.3-13.3(chr1:97410602-110670510)x1 copy number loss See cases [RCV000053877] Chr1:97410602..110670510 [GRCh38]
Chr1:97876158..111213132 [GRCh37]
Chr1:97648746..111014655 [NCBI36]
Chr1:1p21.3-13.3		 pathogenic
NM_001102592.1(HENMT1):c.258G>C (p.Trp86Cys) single nucleotide variant Malignant melanoma [RCV000059827] Chr1:108655591 [GRCh38]
Chr1:109198213 [GRCh37]
Chr1:108999736 [NCBI36]
Chr1:1p13.3		 not provided
GRCh38/hg38 1p21.3-13.3(chr1:97272349-108893138)x1 copy number loss See cases [RCV000135333] Chr1:97272349..108893138 [GRCh38]
Chr1:97737905..109435760 [GRCh37]
Chr1:97510493..109237283 [NCBI36]
Chr1:1p21.3-13.3		 pathogenic
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 1p21.1-13.2(chr1:105468292-112190626)x1 copy number loss See cases [RCV000142760] Chr1:105468292..112190626 [GRCh38]
Chr1:106010914..112733248 [GRCh37]
Chr1:105812437..112534771 [NCBI36]
Chr1:1p21.1-13.2		 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
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 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_001102592.2(HENMT1):c.151G>A (p.Val51Ile) single nucleotide variant Inborn genetic diseases [RCV003292652] Chr1:108655698 [GRCh38]
Chr1:109198320 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.1154A>C (p.Asn385Thr) single nucleotide variant Inborn genetic diseases [RCV003266734] Chr1:108648594 [GRCh38]
Chr1:109191216 [GRCh37]
Chr1:1p13.3		 uncertain significance
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
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
NC_000001.11:g.(?_103175204)_(111410059_?)del deletion Autism [RCV000754122] Chr1:103175204..111410059 [GRCh38]
Chr1:1p21.1-13.2		 likely pathogenic
GRCh37/hg19 1p22.1-13.3(chr1:94054724-111671707)x3 copy number gain not provided [RCV000749068] Chr1:94054724..111671707 [GRCh37]
Chr1:1p22.1-13.3		 pathogenic
NM_001102592.2(HENMT1):c.689G>A (p.Arg230Gln) single nucleotide variant not provided [RCV000901511] Chr1:108650278 [GRCh38]
Chr1:109192900 [GRCh37]
Chr1:1p13.3		 benign
Single allele deletion 1p13.3 deletion syndrome [RCV000786772] Chr1:107779092..111199205 [GRCh37]
Chr1:1p13.3		 likely pathogenic
NM_001102592.2(HENMT1):c.1072A>G (p.Asn358Asp) single nucleotide variant not provided [RCV000961296] Chr1:108648676 [GRCh38]
Chr1:109191298 [GRCh37]
Chr1:1p13.3		 benign
Single allele deletion not provided [RCV000844956] Chr1:108926313..111266497 [GRCh37]
Chr1:1p13.3		 not provided
NC_000001.10:g.(?_108679275)_(111674176_?)del deletion Hereditary spastic paraplegia 63 [RCV003105726] Chr1:108679275..111674176 [GRCh37]
Chr1:1p13.3		 pathogenic
NM_001102592.2(HENMT1):c.114C>T (p.Phe38=) single nucleotide variant not provided [RCV000969404] Chr1:108657487 [GRCh38]
Chr1:109200109 [GRCh37]
Chr1:1p13.3		 benign
GRCh37/hg19 1p13.3(chr1:108769288-109425488)x3 copy number gain not provided [RCV001258447] Chr1:108769288..109425488 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh37/hg19 1p21.2-12(chr1:102021465-119737478) copy number loss Seizure [RCV001352640] Chr1:102021465..119737478 [GRCh37]
Chr1:1p21.2-12		 pathogenic
NM_001102592.2(HENMT1):c.226G>A (p.Gly76Arg) single nucleotide variant Azoospermia [RCV001797578] Chr1:108655623 [GRCh38]
Chr1:109198245 [GRCh37]
Chr1:1p13.3		 pathogenic
NM_001102592.2(HENMT1):c.456C>G (p.Tyr152Ter) single nucleotide variant Azoospermia [RCV001797579] Chr1:108651152 [GRCh38]
Chr1:109193774 [GRCh37]
Chr1:1p13.3		 pathogenic
GRCh37/hg19 1p13.3(chr1:108346477-110177123)x1 copy number loss not provided [RCV001827629] Chr1:108346477..110177123 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh37/hg19 1p21.3-13.2(chr1:95046805-114714931) copy number loss not specified [RCV002053503] Chr1:95046805..114714931 [GRCh37]
Chr1:1p21.3-13.2		 pathogenic
NC_000001.10:g.(?_108679275)_(109493059_?)del deletion not provided [RCV003122418] Chr1:108679275..109493059 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.253C>T (p.Arg85Ter) single nucleotide variant not specified [RCV002247886] Chr1:108655596 [GRCh38]
Chr1:109198218 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.1114C>G (p.Leu372Val) single nucleotide variant Inborn genetic diseases [RCV002794104] Chr1:108648634 [GRCh38]
Chr1:109191256 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.400A>T (p.Ile134Leu) single nucleotide variant Inborn genetic diseases [RCV002779594] Chr1:108651208 [GRCh38]
Chr1:109193830 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.542A>G (p.His181Arg) single nucleotide variant Inborn genetic diseases [RCV002731884] Chr1:108651066 [GRCh38]
Chr1:109193688 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.1151G>A (p.Arg384His) single nucleotide variant Inborn genetic diseases [RCV002977156] Chr1:108648597 [GRCh38]
Chr1:109191219 [GRCh37]
Chr1:1p13.3		 likely benign
NM_001102592.2(HENMT1):c.209G>A (p.Cys70Tyr) single nucleotide variant Inborn genetic diseases [RCV002869759] Chr1:108655640 [GRCh38]
Chr1:109198262 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.366G>T (p.Leu122Phe) single nucleotide variant Inborn genetic diseases [RCV002701940] Chr1:108654748 [GRCh38]
Chr1:109197370 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.1061G>A (p.Arg354His) single nucleotide variant Inborn genetic diseases [RCV002664452] Chr1:108648687 [GRCh38]
Chr1:109191309 [GRCh37]
Chr1:1p13.3		 likely benign
NM_001102592.2(HENMT1):c.589G>T (p.Val197Leu) single nucleotide variant Inborn genetic diseases [RCV002896981] Chr1:108650378 [GRCh38]
Chr1:109193000 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.338G>C (p.Gly113Ala) single nucleotide variant Inborn genetic diseases [RCV003188610] Chr1:108654776 [GRCh38]
Chr1:109197398 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.386C>T (p.Thr129Met) single nucleotide variant Inborn genetic diseases [RCV003197003] Chr1:108654728 [GRCh38]
Chr1:109197350 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.721C>G (p.Leu241Val) single nucleotide variant Inborn genetic diseases [RCV003195844] Chr1:108650246 [GRCh38]
Chr1:109192868 [GRCh37]
Chr1:1p13.3		 likely benign
NM_001102592.2(HENMT1):c.667T>C (p.Cys223Arg) single nucleotide variant Inborn genetic diseases [RCV003285927] Chr1:108650300 [GRCh38]
Chr1:109192922 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.112T>C (p.Phe38Leu) single nucleotide variant Inborn genetic diseases [RCV003357105] Chr1:108657489 [GRCh38]
Chr1:109200111 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.977T>C (p.Ile326Thr) single nucleotide variant Inborn genetic diseases [RCV003364239] Chr1:108648771 [GRCh38]
Chr1:109191393 [GRCh37]
Chr1:1p13.3		 uncertain significance
GRCh37/hg19 1p13.3(chr1:109069332-109366802)x3 copy number gain not provided [RCV003484026] Chr1:109069332..109366802 [GRCh37]
Chr1:1p13.3		 uncertain significance
NM_001102592.2(HENMT1):c.630C>T (p.Val210=) single nucleotide variant not provided [RCV003406639] Chr1:108650337 [GRCh38]
Chr1:109192959 [GRCh37]
Chr1:1p13.3		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:813
Count of miRNA genes:426
Interacting mature miRNAs:464
Transcripts:ENST00000370031, ENST00000370032, ENST00000402983, ENST00000420055, ENST00000483729, ENST00000493676
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.

Markers in Region
RH12040  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371109,190,981 - 109,191,170UniSTSGRCh37
Build 361108,992,504 - 108,992,693RGDNCBI36
Celera1107,460,899 - 107,461,088RGD
Cytogenetic Map1p13.3UniSTS
HuRef1107,083,701 - 107,083,890UniSTS
GeneMap99-GB4 RH Map1336.55UniSTS
NCBI RH Map1832.2UniSTS
G19856  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371109,190,989 - 109,191,151UniSTSGRCh37
Build 361108,992,512 - 108,992,674RGDNCBI36
Celera1107,460,907 - 107,461,069RGD
Cytogenetic Map1p13.3UniSTS
HuRef1107,083,709 - 107,083,871UniSTS
A002A28  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371109,190,989 - 109,191,151UniSTSGRCh37
Build 361108,992,512 - 108,992,674RGDNCBI36
Celera1107,460,907 - 107,461,069RGD
Cytogenetic Map1p13.3UniSTS
HuRef1107,083,709 - 107,083,871UniSTS
TNG Radiation Hybrid Map159362.0UniSTS
GeneMap99-GB4 RH Map1335.76UniSTS


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
Medium 192 283 69 20 835 24 162 29 706 66 620 175 6 3 7 2
Low 2216 2450 1546 499 1080 336 4108 1860 2954 307 812 1387 169 1 1201 2718 2 2
Below cutoff 10 257 99 94 14 94 74 295 11 22 11 22 63 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000370031   ⟹   ENSP00000359048
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,295 - 108,661,055 (-)Ensembl
RefSeq Acc Id: ENST00000370032   ⟹   ENSP00000359049
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,295 - 108,661,526 (-)Ensembl
RefSeq Acc Id: ENST00000402983   ⟹   ENSP00000385655
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,290 - 108,661,122 (-)Ensembl
RefSeq Acc Id: ENST00000420055   ⟹   ENSP00000403953
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,800 - 108,661,180 (-)Ensembl
RefSeq Acc Id: ENST00000483729
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,650,224 - 108,651,445 (-)Ensembl
RefSeq Acc Id: ENST00000493676
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,894 - 108,661,064 (-)Ensembl
RefSeq Acc Id: ENST00000651461   ⟹   ENSP00000499017
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1108,648,295 - 108,661,093 (-)Ensembl
RefSeq Acc Id: NM_001102592   ⟹   NP_001096062
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,648,295 - 108,661,093 (-)NCBI
GRCh371109,190,910 - 109,204,148 (-)RGD
Build 361108,992,433 - 109,005,267 (-)NCBI Archive
Celera1107,460,828 - 107,474,037 (-)RGD
HuRef1107,083,630 - 107,096,727 (-)RGD
CHM1_11109,305,731 - 109,318,557 (-)NCBI
T2T-CHM13v2.01108,681,289 - 108,694,086 (-)NCBI
Sequence:
RefSeq Acc Id: NM_144584   ⟹   NP_653185
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,648,295 - 108,661,474 (-)NCBI
GRCh371109,190,910 - 109,204,148 (-)RGD
Build 361108,992,433 - 109,005,671 (-)NCBI Archive
Celera1107,460,828 - 107,474,037 (-)RGD
HuRef1107,083,630 - 107,096,727 (-)RGD
CHM1_11109,305,731 - 109,318,961 (-)NCBI
T2T-CHM13v2.01108,681,289 - 108,694,467 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005270411   ⟹   XP_005270468
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,648,295 - 108,661,093 (-)NCBI
GRCh371109,190,910 - 109,204,148 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054334063   ⟹   XP_054190038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01108,681,289 - 108,694,086 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_653185   ⟸   NM_144584
- UniProtKB: Q96NN0 (UniProtKB/Swiss-Prot),   Q5T8I9 (UniProtKB/Swiss-Prot),   Q96EJ7 (UniProtKB/Swiss-Prot),   B1AM17 (UniProtKB/Swiss-Prot),   B1AM16 (UniProtKB/Swiss-Prot),   A8MRR6 (UniProtKB/Swiss-Prot),   A0A0A0MRN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001096062   ⟸   NM_001102592
- UniProtKB: Q96NN0 (UniProtKB/Swiss-Prot),   Q5T8I9 (UniProtKB/Swiss-Prot),   Q96EJ7 (UniProtKB/Swiss-Prot),   B1AM17 (UniProtKB/Swiss-Prot),   B1AM16 (UniProtKB/Swiss-Prot),   A8MRR6 (UniProtKB/Swiss-Prot),   A0A0A0MRN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_005270468   ⟸   XM_005270411
- Peptide Label: isoform X1
- UniProtKB: A0A0A0MRN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000359048   ⟸   ENST00000370031
RefSeq Acc Id: ENSP00000359049   ⟸   ENST00000370032
RefSeq Acc Id: ENSP00000499017   ⟸   ENST00000651461
RefSeq Acc Id: ENSP00000385655   ⟸   ENST00000402983
RefSeq Acc Id: ENSP00000403953   ⟸   ENST00000420055
RefSeq Acc Id: XP_054190038   ⟸   XM_054334063
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5T8I9-F1-model_v2 AlphaFold Q5T8I9 1-393 view protein structure

Promoters
RGD ID:6856454
Promoter ID:EPDNEW_H1386
Type:initiation region
Name:HENMT1_1
Description:HEN1 methyltransferase homolog 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1387  EPDNEW_H1388  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,661,075 - 108,661,135EPDNEW
RGD ID:6856444
Promoter ID:EPDNEW_H1387
Type:initiation region
Name:HENMT1_2
Description:HEN1 methyltransferase homolog 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1388  EPDNEW_H1386  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,661,257 - 108,661,317EPDNEW
RGD ID:6856446
Promoter ID:EPDNEW_H1388
Type:initiation region
Name:HENMT1_3
Description:HEN1 methyltransferase homolog 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1387  EPDNEW_H1386  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381108,661,428 - 108,661,488EPDNEW
RGD ID:6784809
Promoter ID:HG_KWN:3929
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000370031,   NM_144584,   OTTHUMT00000030593,   OTTHUMT00000030595,   UC009WER.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361109,005,276 - 109,006,287 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:26400 AgrOrtholog
COSMIC HENMT1 COSMIC
Ensembl Genes ENSG00000162639 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000370031.5 UniProtKB/TrEMBL
  ENST00000370032 ENTREZGENE
  ENST00000370032.9 UniProtKB/Swiss-Prot
  ENST00000402983.5 UniProtKB/Swiss-Prot
  ENST00000420055.1 UniProtKB/TrEMBL
  ENST00000651461 ENTREZGENE
  ENST00000651461.1 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.150 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000162639 GTEx
HGNC ID HGNC:26400 ENTREZGENE
Human Proteome Map HENMT1 Human Proteome Map
InterPro Hen1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:113802 UniProtKB/Swiss-Prot
NCBI Gene 113802 ENTREZGENE
OMIM 612178 OMIM
PANTHER PTHR21404 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMALL RNA 2'-O-METHYLTRANSFERASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Methyltransf_23 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA128394748 PharmGKB
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0A0MRN1 ENTREZGENE, UniProtKB/TrEMBL
  A8MRR6 ENTREZGENE
  B1AM16 ENTREZGENE
  B1AM17 ENTREZGENE
  HENMT_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q96EJ7 ENTREZGENE
  Q96NN0 ENTREZGENE
  X6RGV9_HUMAN UniProtKB/TrEMBL
UniProt Secondary A8MRR6 UniProtKB/Swiss-Prot
  B1AM16 UniProtKB/Swiss-Prot
  B1AM17 UniProtKB/Swiss-Prot
  Q96EJ7 UniProtKB/Swiss-Prot
  Q96NN0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-23 HENMT1  HEN methyltransferase 1    HEN1 methyltransferase homolog 1  Symbol and/or name change 5135510 APPROVED
2016-03-28 HENMT1  HEN1 methyltransferase homolog 1    HEN1 methyltransferase homolog 1 (Arabidopsis)  Symbol and/or name change 5135510 APPROVED
2011-07-27 HENMT1  HEN1 methyltransferase homolog 1 (Arabidopsis)  C1orf59  chromosome 1 open reading frame 59  Symbol and/or name change 5135510 APPROVED