H2BC18 (H2B clustered histone 18) - Rat Genome Database
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Gene: H2BC18 (H2B clustered histone 18) Homo sapiens
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Symbol: H2BC18
Name: H2B clustered histone 18
RGD ID: 1603451
HGNC Page HGNC
Description: Predicted to have DNA binding activity. Predicted to be involved in nucleosome assembly. Localizes to cytosol and nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: FLJ35099; FLJ56780; FLJ56787; HIST2H2BF; histone 2, H2bf; histone cluster 2 H2B family member f; histone cluster 2, H2bf; histone H2B type 2-F; MGC131639
RGD Orthologs
Mouse
Dog
Green Monkey
Alliance Genes
More Info more info ...
Related Pseudogenes: H2BC2P  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1149,782,689 - 149,812,373 (-)EnsemblGRCh38hg38GRCh38
GRCh381149,782,689 - 149,812,370 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371149,754,245 - 149,783,965 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,048,739 - 148,050,535 (-)NCBINCBI36hg18NCBI36
Cytogenetic Map1q21.2NCBI
HuRef1121,197,320 - 121,212,967 (+)NCBIHuRef
CHM1_11151,150,815 - 151,180,499 (-)NCBICHM1_1
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
cytosol  (IDA)
extracellular exosome  (HDA)
nucleoplasm  (IDA,TAS)
nucleosome  (IEA)
nucleus  (HDA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Pipeline to import KEGG annotations from KEGG into RGD
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12408966   PMID:12477932   PMID:12757711   PMID:14702039   PMID:15489334   PMID:16283522   PMID:16307923   PMID:16319397   PMID:16344560   PMID:16710414   PMID:16713563   PMID:16916647  
PMID:19056867   PMID:20458337   PMID:21081503   PMID:21630459   PMID:21873635   PMID:22174317   PMID:22623428   PMID:23254330   PMID:23463506   PMID:25659154   PMID:25963833   PMID:26186194  
PMID:28225217   PMID:28514442   PMID:28902428   PMID:29478914   PMID:29507755   PMID:29845934   PMID:30021884   PMID:30463901   PMID:30575818   PMID:30745168   PMID:31300519   PMID:31980649  


Genomics

Comparative Map Data
H2BC18
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1149,782,689 - 149,812,373 (-)EnsemblGRCh38hg38GRCh38
GRCh381149,782,689 - 149,812,370 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371149,754,245 - 149,783,965 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,048,739 - 148,050,535 (-)NCBINCBI36hg18NCBI36
Cytogenetic Map1q21.2NCBI
HuRef1121,197,320 - 121,212,967 (+)NCBIHuRef
CHM1_11151,150,815 - 151,180,499 (-)NCBICHM1_1
H2bc18
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39396,177,016 - 96,177,508 (+)NCBIGRCm39mm39
GRCm38396,269,700 - 96,270,192 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl396,269,752 - 96,270,132 (+)EnsemblGRCm38mm10GRCm38
MGSCv37396,073,623 - 96,074,115 (+)NCBIGRCm37mm9NCBIm37
MGSCv36396,355,105 - 96,355,597 (+)NCBImm8
Celera397,699,275 - 97,699,767 (+)NCBICelera
Cytogenetic Map3F2.1NCBI
H2BC18
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11759,120,297 - 59,121,083 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
LOC103247165
(Chlorocebus sabaeus - African green monkey)
No map positions available.

Position Markers
GDB:190043  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371149,370,603 - 149,370,937UniSTSGRCh37
GRCh371149,755,559 - 149,755,893UniSTSGRCh37
Build 361147,637,227 - 147,637,561RGDNCBI36
Cytogenetic Map1q21.2-q21.3UniSTS
Cytogenetic Map1q21.2UniSTS
Cytogenetic Map1p11.2UniSTS

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID
MIR99Bhsa-miR-99b-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248

Predicted Target Of
Summary Value
Count of predictions:744
Count of miRNA genes:548
Interacting mature miRNAs:603
Transcripts:ENST00000369167, ENST00000427880, ENST00000469483, ENST00000545683
Prediction methods: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.


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 130 537 143 31 481 15 234 42 128 22 404 445 19 110 69 2
Low 1526 1478 1223 362 992 220 2500 744 2649 246 951 1019 154 1 452 1608 3 2
Below cutoff 781 976 336 208 420 207 1606 1393 956 135 104 146 1 639 1099 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000369167   ⟹   ENSP00000358164
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1149,810,406 - 149,812,359 (-)Ensembl
RefSeq Acc Id: ENST00000420462
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1149,782,877 - 149,811,757 (-)Ensembl
RefSeq Acc Id: ENST00000469483
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1149,803,602 - 149,812,338 (-)Ensembl
RefSeq Acc Id: ENST00000545683   ⟹   ENSP00000445831
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1149,782,689 - 149,812,373 (-)Ensembl
RefSeq Acc Id: ENST00000620458
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl1149,805,260 - 149,812,057 (-)Ensembl
RefSeq Acc Id: NM_001024599   ⟹   NP_001019770
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381149,811,879 - 149,812,370 (-)NCBI
GRCh371149,754,245 - 149,783,965 (-)NCBI
Build 361148,048,739 - 148,050,535 (-)NCBI Archive
HuRef1121,197,320 - 121,212,967 (+)ENTREZGENE
CHM1_11151,180,005 - 151,180,499 (-)NCBI
Sequence:
RefSeq Acc Id: NM_001161334   ⟹   NP_001154806
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381149,782,689 - 149,812,370 (-)NCBI
GRCh371149,754,245 - 149,783,965 (-)NCBI
HuRef1121,197,320 - 121,212,967 (+)ENTREZGENE
CHM1_11151,150,815 - 151,180,499 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001019770   ⟸   NM_001024599
- Peptide Label: isoform a
- UniProtKB: Q5QNW6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001154806   ⟸   NM_001161334
- Peptide Label: isoform b
- UniProtKB: Q5QNW6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000445831   ⟸   ENST00000545683
RefSeq Acc Id: ENSP00000358164   ⟸   ENST00000369167

Promoters
RGD ID:6856914
Promoter ID:EPDNEW_H1622
Type:initiation region
Name:HIST2H2BF_2
Description:histone cluster 2 H2B family member f
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H1625  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381149,812,373 - 149,812,433EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_001161334.1(H2BC18):c.378-964G>A single nucleotide variant IGG receptor I, phagocytic, familial deficiency of [RCV000015950] Chr1:149784224 [GRCh38]
Chr1:149755780 [GRCh37]
Chr1:1q21.2
pathogenic
GRCh37/hg19 1q21.2(chr1:149041013-149768855)x1 copy number loss See cases [RCV000133854] Chr1:149041013..149768855 [GRCh37]
Chr1:147307637..148035479 [NCBI36]
Chr1:1q21.2
benign
GRCh37/hg19 1q21.2(chr1:149041023-149768869)x1 copy number loss See cases [RCV000138911] Chr1:149041023..149768869 [GRCh37]
Chr1:147307647..148035493 [NCBI36]
Chr1:1q21.2
benign
GRCh37/hg19 1q21.2(chr1:149783688-150049029)x3 copy number gain Ductal breast carcinoma [RCV000207055] Chr1:149783688..150049029 [GRCh37]
Chr1:1q21.2
uncertain significance
GRCh37/hg19 1q21.1-21.3(chr1:144927578-153223600)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV000223957] Chr1:144927578..153223600 [GRCh37]
Chr1:1q21.1-21.3
pathogenic
GRCh37/hg19 1q21.1-21.2(chr1:143500223-149763815)x3 copy number gain See cases [RCV000240518] Chr1:143500223..149763815 [GRCh37]
Chr1:1q21.1-21.2
pathogenic
GRCh37/hg19 1q21.2(chr1:149754410-149763756)x1 copy number loss See cases [RCV000449320] Chr1:149754410..149763756 [GRCh37]
Chr1:1q21.2
benign
GRCh37/hg19 1q21.1-21.3(chr1:143753740-151399970)x3 copy number gain See cases [RCV000447109] Chr1:143753740..151399970 [GRCh37]
Chr1:1q21.1-21.3
pathogenic
GRCh37/hg19 1q21.2(chr1:149223984-149763756)x3 copy number gain See cases [RCV000446905] Chr1:149223984..149763756 [GRCh37]
Chr1:1q21.2
likely benign
GRCh37/hg19 1q21.2(chr1:148004766-149754410)x3 copy number gain See cases [RCV000447369] Chr1:148004766..149754410 [GRCh37]
Chr1:1q21.2
benign
GRCh37/hg19 1q21.2(chr1:148940709-149763756)x1 copy number loss See cases [RCV000447878] Chr1:148940709..149763756 [GRCh37]
Chr1:1q21.2
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 1q21.1-21.2(chr1:143932350-149801420)x3 copy number gain See cases [RCV000511264] Chr1:143932350..149801420 [GRCh37]
Chr1:1q21.1-21.2
likely pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
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
NM_000566.3(FCGR1A):c.21G>A (p.Leu7=) single nucleotide variant not provided [RCV000948557] Chr1:149782764 [GRCh38]
Chr1:149754320 [GRCh37]
Chr1:1q21.2
likely benign
NM_000566.3(FCGR1A):c.114C>T (p.Thr38=) single nucleotide variant not provided [RCV000973282] Chr1:149784064 [GRCh38]
Chr1:149755620 [GRCh37]
Chr1:1q21.2
likely benign
NM_000566.3(FCGR1A):c.736C>T (p.Gln246Ter) single nucleotide variant Peritoneal Gliomatosis [RCV000852293] Chr1:149790230 [GRCh38]
Chr1:149761786 [GRCh37]
Chr1:1q21.2
uncertain significance
NM_001161334.1(H2BC18):c.378-8204_378-8202del microsatellite not provided [RCV000910018] Chr1:149791462..149791464 [GRCh38]
Chr1:149763018..149763020 [GRCh37]
Chr1:1q21.2
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:24700 AgrOrtholog
COSMIC H2BC18 COSMIC
Ensembl Genes ENSG00000203814 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000358164 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000445831 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000369167 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000545683 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
GTEx ENSG00000203814 GTEx
HGNC ID HGNC:24700 ENTREZGENE
Human Proteome Map H2BC18 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H2B UniProtKB/Swiss-Prot
KEGG Report hsa:440689 UniProtKB/Swiss-Prot
NCBI Gene 440689 ENTREZGENE
PANTHER PTHR23428 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PharmGKB PA145148722 PharmGKB
PRINTS HISTONEH2B UniProtKB/Swiss-Prot
PROSITE HISTONE_H2B UniProtKB/Swiss-Prot
SMART H2B UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniProt H2B2F_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A8K0U9 UniProtKB/Swiss-Prot
  B4DLA9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2BC18  H2B clustered histone 18  HIST2H2BF  histone cluster 2 H2B family member f  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST2H2BF  histone cluster 2 H2B family member f    histone cluster 2, H2bf  Symbol and/or name change 5135510 APPROVED