H3C13 (H3 clustered histone 13) - Rat Genome Database

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Gene: H3C13 (H3 clustered histone 13) Homo sapiens
Analyze
Symbol: H3C13
Name: H3 clustered histone 13
RGD ID: 1604125
HGNC Page HGNC:25311
Description: Predicted to enable DNA binding activity and protein heterodimerization activity. Predicted to be a structural constituent of chromatin. Involved in nucleosome assembly. Located in nucleoplasm. Part of nucleosome.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: H3-clustered histone 14; H3-clustered histone 15; H3C14; H3C15; HIST2H3A; HIST2H3C; HIST2H3D; histone 2, H3d; histone cluster 2 H3 family member d; histone cluster 2, H3d; histone H3.2; histone H3/m; histone H3/o
RGD Orthologs
Mouse
Rat
Dog
Alliance Orthologs
More Info more info ...
Related Pseudogenes: H3C9P   H3P4  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381149,813,225 - 149,813,693 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1149,813,225 - 149,813,693 (-)EnsemblGRCh38hg38GRCh38
GRCh371149,784,780 - 149,785,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,051,450 - 148,051,860 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map1q21.2NCBI
CHM1_11151,181,351 - 151,181,807 (-)NCBICHM1_1
T2T-CHM13v2.01148,937,360 - 148,937,828 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (IEA)
chromosome  (IEA)
extracellular exosome  (HDA)
extracellular region  (TAS)
nucleoplasm  (IDA,TAS)
nucleosome  (IDA,IEA,IPI)
nucleus  (HDA,IDA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12408966   PMID:17353931   PMID:17967883   PMID:18029348   PMID:19199708   PMID:20458337   PMID:20580717   PMID:21081503   PMID:21489993   PMID:21596426   PMID:21630459   PMID:21636898  
PMID:21873635   PMID:22623428   PMID:23075851   PMID:24625528   PMID:24711643   PMID:25416818   PMID:25615412   PMID:25963833   PMID:26167883   PMID:26687479   PMID:26694698   PMID:27248496  
PMID:28718761   PMID:28977666   PMID:29128334   PMID:29478914   PMID:29507755   PMID:29676528   PMID:29778605   PMID:30021884   PMID:30209976   PMID:30575818   PMID:31353912   PMID:31790919  
PMID:32296183   PMID:32814053   PMID:33080218   PMID:33857403   PMID:33961781   PMID:34079125   PMID:34244791   PMID:34373451   PMID:35271311   PMID:36180920   PMID:36835656   PMID:36949045  


Genomics

Comparative Map Data
H3C13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381149,813,225 - 149,813,693 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1149,813,225 - 149,813,693 (-)EnsemblGRCh38hg38GRCh38
GRCh371149,784,780 - 149,785,248 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361148,051,450 - 148,051,860 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map1q21.2NCBI
CHM1_11151,181,351 - 151,181,807 (-)NCBICHM1_1
T2T-CHM13v2.01148,937,360 - 148,937,828 (-)NCBIT2T-CHM13v2.0
H3c3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,929,025 - 23,929,504 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,928,956 - 23,929,585 (-)EnsemblGRCm39 Ensembl
GRCm381323,745,042 - 23,745,521 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,744,973 - 23,745,602 (-)EnsemblGRCm38mm10GRCm38
MGSCv371323,836,911 - 23,837,390 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,752,507 - 23,752,986 (-)NCBIMGSCv36mm8
Celera1323,976,813 - 23,977,292 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
cM Map139.9NCBI
H3c13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81741,959,540 - 41,960,009 (-)NCBIGRCr8
mRatBN7.21741,531,502 - 41,531,971 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1741,369,308 - 41,386,656 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl2183,809,711 - 183,810,382 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1741,378,175 - 41,378,719 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl1741,560,880 - 41,561,441 (-)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl2183,837,303 - 183,837,752 (+)EnsemblmRatBN7.2 Ensembl
mRatBN7.2 Ensembl2183,795,504 - 183,809,469 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01743,776,018 - 43,776,779 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01745,633,008 - 45,635,861 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,162,388 - 41,163,357 (-)NCBICelera
Cytogenetic Map17p11NCBI
H3C13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11759,121,020 - 59,129,410 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1759,121,976 - 59,122,386 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1758,556,954 - 58,577,480 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01760,105,729 - 60,112,244 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11758,955,305 - 58,975,896 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01759,039,033 - 59,059,561 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01759,765,907 - 59,786,436 (-)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in H3C13
12 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh37/hg19 1q21.2(chr1:149783688-150049029)x3 copy number gain Breast ductal adenocarcinoma [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 1q21.1-21.3(chr1:143753740-151399970)x3 copy number gain See cases [RCV000447109] Chr1:143753740..151399970 [GRCh37]
Chr1:1q21.1-21.3		 pathogenic
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_001123375.3(H3C13):c.198G>A (p.Leu66=) single nucleotide variant not provided [RCV000974858] Chr1:149813484 [GRCh38]
Chr1:149785039 [GRCh37]
Chr1:1q21.2		 benign
NM_001123375.3(H3C13):c.174T>C (p.Ser58=) single nucleotide variant not provided [RCV000892460] Chr1:149813508 [GRCh38]
Chr1:149785063 [GRCh37]
Chr1:1q21.2		 benign
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NC_000001.11:g.145516559_149951620del deletion Cataract 46 juvenile-onset [RCV004787127] Chr1:145516559..149951620 [GRCh38]
Chr1:1q21.1-21.2		 uncertain significance
NM_001123375.3(H3C13):c.67A>G (p.Thr23Ala) single nucleotide variant not specified [RCV004325244] Chr1:149813615 [GRCh38]
Chr1:149785170 [GRCh37]
Chr1:1q21.2		 uncertain significance
GRCh37/hg19 1q12-23.1(chr1:142535935-157648813)x3 copy number gain Chromosome 1q21.1 duplication syndrome [RCV003329522] Chr1:142535935..157648813 [GRCh37]
Chr1:1q12-23.1		 pathogenic
NM_001123375.3(H3C13):c.240G>C (p.Lys80Asn) single nucleotide variant not specified [RCV004334428] Chr1:149813442 [GRCh38]
Chr1:149784997 [GRCh37]
Chr1:1q21.2		 uncertain significance
GRCh37/hg19 1q21.1-23.1(chr1:144368497-158992086)x3 copy number gain not specified [RCV003986717] Chr1:144368497..158992086 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
GRCh37/hg19 1q21.2-21.3(chr1:149713775-150385573)x1 copy number loss not specified [RCV003986097] Chr1:149713775..150385573 [GRCh37]
Chr1:1q21.2-21.3		 pathogenic
GRCh37/hg19 1q21.1-23.1(chr1:146577511-157155587)x3 copy number gain not specified [RCV003987261] Chr1:146577511..157155587 [GRCh37]
Chr1:1q21.1-23.1		 pathogenic
NM_001123375.3(H3C13):c.262T>C (p.Ser88Pro) single nucleotide variant not specified [RCV004396738] Chr1:149813420 [GRCh38]
Chr1:149784975 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.329T>A (p.Leu110Gln) single nucleotide variant not specified [RCV004396739] Chr1:149813353 [GRCh38]
Chr1:149784908 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.370G>A (p.Asp124Asn) single nucleotide variant not specified [RCV004396740] Chr1:149813312 [GRCh38]
Chr1:149784867 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.209G>A (p.Arg70Gln) single nucleotide variant not specified [RCV004396737] Chr1:149813473 [GRCh38]
Chr1:149785028 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.230A>T (p.Gln77Leu) single nucleotide variant not specified [RCV004627326] Chr1:149813452 [GRCh38]
Chr1:149785007 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.116C>T (p.Pro39Leu) single nucleotide variant not specified [RCV004627327] Chr1:149813566 [GRCh38]
Chr1:149785121 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.363G>A (p.Met121Ile) single nucleotide variant not specified [RCV004917228] Chr1:149813319 [GRCh38]
Chr1:149784874 [GRCh37]
Chr1:1q21.2		 uncertain significance
NM_001123375.3(H3C13):c.223A>G (p.Ile75Val) single nucleotide variant not specified [RCV004930757] Chr1:149813459 [GRCh38]
Chr1:149785014 [GRCh37]
Chr1:1q21.2		 uncertain significance

QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357381BW57_HBody weight QTL 57 (human)10.0001Body weightfat free mass after exercise training1140630236166630236Human

Markers in Region
RH66497  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371149,834,384 - 149,834,524UniSTSGRCh37
GRCh371149,802,422 - 149,802,562UniSTSGRCh37
Build 361148,069,046 - 148,069,186RGDNCBI36
Cytogenetic Map1q21.2UniSTS
Cytogenetic Map1q21UniSTS
HuRef1121,217,105 - 121,217,245UniSTS
HuRef1121,185,132 - 121,185,272UniSTS
GeneMap99-GB4 RH Map1536.52UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENST00000331491   ⟹   ENSP00000333277
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1149,813,225 - 149,813,693 (-)Ensembl
RefSeq Acc Id: NM_001123375   ⟹   NP_001116847
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381149,813,225 - 149,813,693 (-)NCBI
GRCh371149,784,780 - 149,785,236 (-)ENTREZGENE
CHM1_11151,181,351 - 151,181,807 (-)NCBI
T2T-CHM13v2.01148,937,360 - 148,937,828 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001116847 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAI12559 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000333277
  ENSP00000333277.2
  ENSP00000358154.1
  ENSP00000385479.1
GenBank Protein Q71DI3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001116847   ⟸   NM_001123375
- UniProtKB: A6NFS4 (UniProtKB/Swiss-Prot),   A2BDF6 (UniProtKB/Swiss-Prot),   Q6B053 (UniProtKB/Swiss-Prot),   Q71DI3 (UniProtKB/Swiss-Prot),   A8K4Y7 (UniProtKB/TrEMBL),   B2R6Y1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000333277   ⟸   ENST00000331491
Protein Domains
Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q71DI3-F1-model_v2 AlphaFold Q71DI3 1-136 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:25311 AgrOrtholog
COSMIC H3C13 COSMIC
Ensembl Genes ENSG00000183598 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000203811 UniProtKB/Swiss-Prot
  ENSG00000203852 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000331491 ENTREZGENE
  ENST00000331491.2 UniProtKB/Swiss-Prot
  ENST00000369158.2 UniProtKB/Swiss-Prot
  ENST00000403683.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
GTEx ENSG00000183598 GTEx
  ENSG00000203811 GTEx
  ENSG00000203852 GTEx
HGNC ID HGNC:25311 ENTREZGENE
Human Proteome Map H3C13 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H3/CENP-A UniProtKB/Swiss-Prot
KEGG Report hsa:126961 UniProtKB/Swiss-Prot
  hsa:333932 UniProtKB/Swiss-Prot
  hsa:653604 UniProtKB/Swiss-Prot
NCBI Gene 653604 ENTREZGENE
PANTHER PTHR11426 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PharmGKB PA166351898 PharmGKB
PRINTS HISTONEH3 UniProtKB/Swiss-Prot
PROSITE HISTONE_H3_1 UniProtKB/Swiss-Prot
  HISTONE_H3_2 UniProtKB/Swiss-Prot
SMART SM00428 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniProt A2BDF6 ENTREZGENE
  A6NFS4 ENTREZGENE
  A8K4Y7 ENTREZGENE, UniProtKB/TrEMBL
  B2R6Y1 ENTREZGENE, UniProtKB/TrEMBL
  H32_HUMAN UniProtKB/Swiss-Prot
  Q6B053 ENTREZGENE
  Q71DI3 ENTREZGENE
UniProt Secondary A2BDF6 UniProtKB/Swiss-Prot
  A6NFS4 UniProtKB/Swiss-Prot
  Q6B053 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H3C13  H3 clustered histone 13  HIST2H3D  histone cluster 2 H3 family member d  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST2H3D  histone cluster 2 H3 family member d    histone cluster 2, H3d  Symbol and/or name change 5135510 APPROVED