H2AC15 (H2A clustered histone 15) - Rat Genome Database

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Pathways
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Gene: H2AC15 (H2A clustered histone 15) Homo sapiens
Analyze
Symbol: H2AC15
Name: H2A clustered histone 15
RGD ID: 1312612
HGNC Page HGNC:4726
Description: Enables enzyme binding activity. Predicted to be involved in heterochromatin organization. Located in nucleus.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: H2A histone family, member D; H2A.1; H2A/d; H2AC11; H2AC13; H2AC14; H2AC16; H2AC17; H2AFD; HIST1H2AG; HIST1H2AJ; HIST1H2AK; HIST1H2AL; HIST1H2AM; histone 1, H2ak; histone cluster 1 H2A family member k; histone cluster 1, H2ak; histone H2A type 1; histone H2A type 1-J; histone H2A/e; histone H2A/p; histone H2A/ptl
RGD Orthologs
Mouse
Dog
Alliance Genes
More Info more info ...
Related Pseudogenes: H2ACP1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38627,837,880 - 27,838,375 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl627,837,880 - 27,838,375 (-)EnsemblGRCh38hg38GRCh38
GRCh37627,805,658 - 27,806,153 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,913,605 - 27,914,103 (-)NCBINCBI36Build 36hg18NCBI36
Build 34627,913,636 - 27,914,096NCBI
Celera629,411,662 - 29,412,160 (-)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef627,613,312 - 27,613,771 (-)NCBIHuRef
CHM1_1627,807,805 - 27,808,264 (-)NCBICHM1_1
T2T-CHM13v2.0627,707,553 - 27,708,048 (-)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
chromosome  (IEA)
extracellular exosome  (HDA)
intracellular organelle  (IEA)
nucleosome  (IBA,IEA)
nucleus  (HDA,IBA,IDA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9439656   PMID:9566873   PMID:10064132   PMID:11080476   PMID:11689053   PMID:12408966   PMID:12477932   PMID:14574404   PMID:14657027   PMID:15010469   PMID:15078818   PMID:15161933  
PMID:15386022   PMID:15489334   PMID:15635413   PMID:15823041   PMID:16319397   PMID:16359901   PMID:16457589   PMID:16702407   PMID:17980597   PMID:18688256   PMID:20458337   PMID:20618440  
PMID:21145461   PMID:21179169   PMID:21630459   PMID:21873635   PMID:22194607   PMID:23533145   PMID:25281266   PMID:25416956   PMID:25963833   PMID:26647312   PMID:26687479   PMID:29507755  
PMID:33080218   PMID:36180920  


Genomics

Comparative Map Data
H2AC15
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38627,837,880 - 27,838,375 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl627,837,880 - 27,838,375 (-)EnsemblGRCh38hg38GRCh38
GRCh37627,805,658 - 27,806,153 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36627,913,605 - 27,914,103 (-)NCBINCBI36Build 36hg18NCBI36
Build 34627,913,636 - 27,914,096NCBI
Celera629,411,662 - 29,412,160 (-)NCBICelera
Cytogenetic Map6p22.1NCBI
HuRef627,613,312 - 27,613,771 (-)NCBIHuRef
CHM1_1627,807,805 - 27,808,264 (-)NCBICHM1_1
T2T-CHM13v2.0627,707,553 - 27,708,048 (-)NCBIT2T-CHM13v2.0
H2ac6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391323,867,456 - 23,867,942 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1323,865,450 - 23,867,931 (-)EnsemblGRCm39 Ensembl
GRCm381323,683,473 - 23,683,959 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1323,681,467 - 23,683,948 (-)EnsemblGRCm38mm10GRCm38
MGSCv371323,773,336 - 23,775,828 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361323,688,932 - 23,691,424 (-)NCBIMGSCv36mm8
Celera1323,912,758 - 23,915,252 (-)NCBICelera
Cytogenetic Map13A3.1NCBI
cM Map139.87NCBI
H2AC19
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11759,156,821 - 59,157,523 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1759,147,111 - 59,147,503 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1758,594,993 - 58,595,586 (-)NCBIDog10K_Boxer_Tasha

Variants

.
Variants in H2AC15
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 6p22.3-21.33(chr6:18120520-30767516)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052180]|See cases [RCV000052180] Chr6:18120520..30767516 [GRCh38]
Chr6:18120751..30735293 [GRCh37]
Chr6:18228730..30843272 [NCBI36]
Chr6:6p22.3-21.33		 pathogenic
GRCh38/hg38 6p22.2-22.1(chr6:26280579-28727313)x3 copy number gain See cases [RCV000133692] Chr6:26280579..28727313 [GRCh38]
Chr6:26280807..28695090 [GRCh37]
Chr6:26388786..28803069 [NCBI36]
Chr6:6p22.2-22.1		 uncertain significance
GRCh38/hg38 6p25.2-21.33(chr6:3224310-30657190)x3 copy number gain See cases [RCV000138956] Chr6:3224310..30657190 [GRCh38]
Chr6:3224544..30624967 [GRCh37]
Chr6:3169543..30732946 [NCBI36]
Chr6:6p25.2-21.33		 pathogenic
GRCh38/hg38 6p25.3-12.3(chr6:156974-46789291)x3 copy number gain See cases [RCV000143497] Chr6:156974..46789291 [GRCh38]
Chr6:156974..46757028 [GRCh37]
Chr6:101974..46864987 [NCBI36]
Chr6:6p25.3-12.3		 pathogenic
GRCh37/hg19 6p22.1(chr6:27775494-27861432)x3 copy number gain Breast ductal adenocarcinoma [RCV000207227] Chr6:27775494..27861432 [GRCh37]
Chr6:6p22.1		 uncertain significance
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482)x3 copy number gain See cases [RCV000512067] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:156975-170919482) copy number gain See cases [RCV000510595] Chr6:156975..170919482 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:108666-170980171)x3 copy number gain not provided [RCV000745403] Chr6:108666..170980171 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:60107-171054786)x3 copy number gain not provided [RCV000745400] Chr6:60107..171054786 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p25.3-q27(chr6:165632-170919470)x3 copy number gain not provided [RCV000745404] Chr6:165632..170919470 [GRCh37]
Chr6:6p25.3-q27		 pathogenic
GRCh37/hg19 6p22.1(chr6:27609423-28016099)x3 copy number gain not provided [RCV000745576] Chr6:27609423..28016099 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27645278-27902992)x3 copy number gain not provided [RCV000745579] Chr6:27645278..27902992 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27710165-27885437)x3 copy number gain not provided [RCV000745581] Chr6:27710165..27885437 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27713299-27872832)x3 copy number gain not provided [RCV000745582] Chr6:27713299..27872832 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27871553)x3 copy number gain not provided [RCV000745583] Chr6:27715243..27871553 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27877446)x3 copy number gain not provided [RCV000745584] Chr6:27715243..27877446 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715243-27890631)x3 copy number gain not provided [RCV000745585] Chr6:27715243..27890631 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27715470-27886830)x3 copy number gain not provided [RCV000745586] Chr6:27715470..27886830 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27745142-27870358)x3 copy number gain not provided [RCV000745587] Chr6:27745142..27870358 [GRCh37]
Chr6:6p22.1		 benign
GRCh37/hg19 6p22.1(chr6:27616157-28011557)x3 copy number gain not provided [RCV001005790] Chr6:27616157..28011557 [GRCh37]
Chr6:6p22.1		 likely benign
NM_003510.3(H2AC15):c.67G>T (p.Gly23Cys) single nucleotide variant Inborn genetic diseases [RCV003206039] Chr6:27838273 [GRCh38]
Chr6:27806051 [GRCh37]
Chr6:6p22.1		 uncertain significance
NM_003510.3(H2AC15):c.35G>A (p.Arg12His) single nucleotide variant Inborn genetic diseases [RCV003378640] Chr6:27838305 [GRCh38]
Chr6:27806083 [GRCh37]
Chr6:6p22.1		 uncertain significance
GRCh37/hg19 6p22.1(chr6:27613035-28021256)x3 copy number gain not specified [RCV003986654] Chr6:27613035..28021256 [GRCh37]
Chr6:6p22.1		 uncertain significance
Markers in Region
AL021849  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,804,873 - 27,805,030UniSTSGRCh37
Build 36627,912,852 - 27,913,009RGDNCBI36
Celera629,410,909 - 29,411,066RGD
Cytogenetic Map6p22.1UniSTS
HuRef627,612,527 - 27,612,684UniSTS
UniSTS:487023  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,806,440 - 27,806,870UniSTSGRCh37
Build 36627,914,419 - 27,914,849RGDNCBI36
Celera629,412,476 - 29,412,906RGD
HuRef627,614,094 - 27,614,524UniSTS
UniSTS:489748  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37627,805,675 - 27,806,117UniSTSGRCh37
Build 36627,913,654 - 27,914,096RGDNCBI36
Celera629,411,711 - 29,412,153RGD
HuRef627,613,329 - 27,613,771UniSTS


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 adipose tissue appendage
High
Medium 1 15 15 4 40 1
Low 1628 2941 796 128 2369 80 1329 467 716 25 1175 1374 48 365 926
Below cutoff 2461 2931 1891 622 948 321 5478 2390 4860 179 1267 1345 301 1796 3562

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000618958   ⟹   ENSP00000482431
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl627,837,880 - 27,838,375 (-)Ensembl
RefSeq Acc Id: NM_003510   ⟹   NP_003501
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38627,837,880 - 27,838,375 (-)NCBI
GRCh37627,805,658 - 27,806,117 (-)ENTREZGENE
Build 36627,913,637 - 27,914,096 (-)NCBI Archive
Celera629,411,662 - 29,412,160 (-)RGD
HuRef627,613,312 - 27,613,771 (-)ENTREZGENE
CHM1_1627,807,805 - 27,808,264 (-)NCBI
T2T-CHM13v2.0627,707,553 - 27,708,048 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_003501   ⟸   NM_003510
- UniProtKB: Q2M1R2 (UniProtKB/Swiss-Prot),   P02261 (UniProtKB/Swiss-Prot),   Q76PA6 (UniProtKB/Swiss-Prot),   P0C0S8 (UniProtKB/Swiss-Prot),   A4FTV9 (UniProtKB/TrEMBL),   B2R5B3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000482431   ⟸   ENST00000618958
Protein Domains
Histone H2A C-terminal   Histone H2A/H2B/H3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q99878-F1-model_v2 AlphaFold Q99878 1-128 view protein structure
AF-P0C0S8-F1-model_v2 AlphaFold P0C0S8 1-130 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:4726 AgrOrtholog
COSMIC H2AC15 COSMIC
Ensembl Genes ENSG00000196747 UniProtKB/Swiss-Prot
  ENSG00000196787 UniProtKB/Swiss-Prot
  ENSG00000275221 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSG00000276903 UniProtKB/Swiss-Prot
  ENSG00000278677 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000358739.5 UniProtKB/Swiss-Prot
  ENST00000359193.4 UniProtKB/Swiss-Prot
  ENST00000359611.4 UniProtKB/Swiss-Prot
  ENST00000613174.2 UniProtKB/Swiss-Prot
  ENST00000618958 ENTREZGENE
  ENST00000618958.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000196747 GTEx
  ENSG00000196787 GTEx
  ENSG00000275221 GTEx
  ENSG00000276903 GTEx
  ENSG00000278677 GTEx
HGNC ID HGNC:4726 ENTREZGENE
Human Proteome Map H2AC15 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8329 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8332 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8336 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  hsa:8969 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8330 ENTREZGENE
OMIM 602788 OMIM
PANTHER HISTONE H2A.J UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23430 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Histone UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Histone_H2A_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PRINTS HISTONEH2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HISTONE_H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART H2A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A4FTV9 ENTREZGENE, UniProtKB/TrEMBL
  B2R5B3 ENTREZGENE
  H2A1_HUMAN UniProtKB/Swiss-Prot
  P02261 ENTREZGENE
  P0C0S8 ENTREZGENE
  Q2M1R2 ENTREZGENE
  Q76PA6 ENTREZGENE
UniProt Secondary P02261 UniProtKB/Swiss-Prot
  Q2M1R2 UniProtKB/Swiss-Prot
  Q76PA6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-07-30 H2AC15  H2A clustered histone 15  HIST1H2AK  histone cluster 1 H2A family member k  Symbol and/or name change 5135510 APPROVED
2016-08-23 HIST1H2AK  histone cluster 1 H2A family member k  HIST1H2AK  histone cluster 1, H2ak  Symbol and/or name change 5135510 APPROVED