C3orf84 (chromosome 3 open reading frame 84) - Rat Genome Database

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Gene: C3orf84 (chromosome 3 open reading frame 84) Homo sapiens
Analyze
Symbol: C3orf84
Name: chromosome 3 open reading frame 84
RGD ID: 7254257
HGNC Page HGNC:44666
Description: ASSOCIATED WITH Aicardi-Goutieres Syndrome 1; genetic disease; Pierson syndrome; INTERACTS WITH Aflatoxin B2 alpha; benzo[a]pyrene; bisphenol A (ortholog)
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: uncharacterized protein C3orf84; uncharacterized protein LOC646498
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38349,177,634 - 49,191,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl349,177,634 - 49,191,858 (-)EnsemblGRCh38hg38GRCh38
GRCh37349,215,067 - 49,229,291 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,190,073 - 49,204,114 (-)NCBINCBI36Build 36hg18NCBI36
Celera349,172,338 - 49,184,925 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef349,273,028 - 49,287,244 (-)NCBIHuRef
CHM1_1349,167,840 - 49,182,055 (-)NCBICHM1_1
T2T-CHM13v2.0349,205,607 - 49,219,926 (-)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

Molecular Function

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

Genomics

Comparative Map Data
C3orf84
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38349,177,634 - 49,191,858 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl349,177,634 - 49,191,858 (-)EnsemblGRCh38hg38GRCh38
GRCh37349,215,067 - 49,229,291 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36349,190,073 - 49,204,114 (-)NCBINCBI36Build 36hg18NCBI36
Celera349,172,338 - 49,184,925 (-)NCBICelera
Cytogenetic Map3p21.31NCBI
HuRef349,273,028 - 49,287,244 (-)NCBIHuRef
CHM1_1349,167,840 - 49,182,055 (-)NCBICHM1_1
T2T-CHM13v2.0349,205,607 - 49,219,926 (-)NCBIT2T-CHM13v2.0
BC048562
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399108,313,681 - 108,323,282 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9108,313,681 - 108,323,285 (+)EnsemblGRCm39 Ensembl
GRCm389108,436,482 - 108,446,083 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9108,436,482 - 108,446,086 (+)EnsemblGRCm38mm10GRCm38
MGSCv379108,338,813 - 108,348,414 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369108,294,585 - 108,304,189 (+)NCBIMGSCv36mm8
Celera9108,045,624 - 108,055,271 (+)NCBICelera
Cytogenetic Map9F2NCBI
cM Map959.35NCBI
C8h3orf84
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88118,002,336 - 118,019,337 (+)NCBIGRCr8
mRatBN7.28109,131,138 - 109,140,784 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8109,124,762 - 109,140,791 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8114,752,720 - 114,762,393 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08112,952,051 - 112,961,724 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08110,794,701 - 110,804,374 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08117,214,999 - 117,231,024 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8117,221,367 - 117,231,029 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08116,565,953 - 116,575,596 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera8108,431,733 - 108,441,366 (+)ENTREZGENECelera
Cytogenetic Map8q32NCBI
CUNH3orf84
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555321,163,353 - 1,198,237 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555321,163,399 - 1,172,197 (-)NCBIChiLan1.0ChiLan1.0
C2H3orf84
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2249,155,473 - 49,169,640 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1349,160,239 - 49,174,495 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0349,100,962 - 49,115,215 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1350,180,907 - 50,195,215 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl350,180,907 - 50,195,215 (-)Ensemblpanpan1.1panPan2
C20H3orf84
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12040,012,730 - 40,021,983 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2040,012,854 - 40,021,981 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2039,930,901 - 39,940,154 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02040,369,593 - 40,378,845 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2040,369,716 - 40,378,843 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12039,736,506 - 39,745,708 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02040,139,971 - 40,149,223 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02040,420,245 - 40,429,496 (+)NCBIUU_Cfam_GSD_1.0
CUNH3orf84
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560264,112,332 - 64,124,399 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936529872,837 - 884,879 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936529872,150 - 884,123 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C13H3orf84
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1331,780,277 - 31,792,782 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11331,780,619 - 31,790,704 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21335,011,821 - 35,023,160 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH3orf84
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12210,579,771 - 10,594,148 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2210,579,776 - 10,593,388 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041156,499,978 - 156,501,477 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
CUNH3orf84
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247303,188,765 - 3,198,025 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247303,187,956 - 3,198,064 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in C3orf84
4 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_173546.2(KLHDC8B):c.766+30C>T single nucleotide variant Malignant melanoma [RCV000066115] Chr3:49174996 [GRCh38]
Chr3:49212429 [GRCh37]
Chr3:49187433 [NCBI36]
Chr3:3p21.31		 not provided
GRCh38/hg38 3p21.31-21.2(chr3:45879883-50749922)x4 copy number gain See cases [RCV000133650] Chr3:45879883..50749922 [GRCh38]
Chr3:45921375..50787353 [GRCh37]
Chr3:45896379..50762357 [NCBI36]
Chr3:3p21.31-21.2		 pathogenic
GRCh38/hg38 3p21.31(chr3:49171381-49474635)x3 copy number gain See cases [RCV000143511] Chr3:49171381..49474635 [GRCh38]
Chr3:49208814..49512068 [GRCh37]
Chr3:49183818..49487072 [NCBI36]
Chr3:3p21.31		 uncertain significance
GRCh37/hg19 3p22.2-21.31(chr3:37028313-49929220)x3 copy number gain See cases [RCV000240519] Chr3:37028313..49929220 [GRCh37]
Chr3:3p22.2-21.31		 likely pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986)x3 copy number gain See cases [RCV000511055] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61892-197851986) copy number gain See cases [RCV000512358] Chr3:61892..197851986 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:61495-197838262)x3 copy number gain not provided [RCV000742138] Chr3:61495..197838262 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p26.3-q29(chr3:60174-197948027)x3 copy number gain not provided [RCV000742133] Chr3:60174..197948027 [GRCh37]
Chr3:3p26.3-q29		 pathogenic
GRCh37/hg19 3p21.31-21.1(chr3:45153770-53878616) copy number gain not provided [RCV000767704] Chr3:45153770..53878616 [GRCh37]
Chr3:3p21.31-21.1		 pathogenic
GRCh37/hg19 3p21.31(chr3:48346677-49630228)x1 copy number loss not provided [RCV001005432] Chr3:48346677..49630228 [GRCh37]
Chr3:3p21.31		 pathogenic
NC_000003.12:g.(?_49121216)_(49533209_?)del deletion Pierson syndrome [RCV001384888] Chr3:49158649..49570642 [GRCh37]
Chr3:3p21.31		 pathogenic
GRCh37/hg19 3p21.31-21.2(chr3:48807193-51363558)x1 copy number loss not provided [RCV001259686] Chr3:48807193..51363558 [GRCh37]
Chr3:3p21.31-21.2		 pathogenic
NC_000003.11:g.(?_48507870)_(50340407_?)del deletion Aicardi-Goutieres syndrome 1 [RCV001380369] Chr3:48507870..50340407 [GRCh37]
Chr3:3p21.31		 pathogenic
GRCh37/hg19 3p21.31(chr3:49060512-49678685) copy number gain not specified [RCV002053349] Chr3:49060512..49678685 [GRCh37]
Chr3:3p21.31		 uncertain significance
NM_001080528.3(C3orf84):c.148G>A (p.Ala50Thr) single nucleotide variant Inborn genetic diseases [RCV002752235] Chr3:49178532 [GRCh38]
Chr3:49215965 [GRCh37]
Chr3:3p21.31		 uncertain significance
NM_001080528.3(C3orf84):c.460C>T (p.His154Tyr) single nucleotide variant Inborn genetic diseases [RCV002762571] Chr3:49177791 [GRCh38]
Chr3:49215224 [GRCh37]
Chr3:3p21.31		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:861
Count of miRNA genes:264
Interacting mature miRNAs:275
Transcripts:ENST00000432035, ENST00000443990, ENST00000545770
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.


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 1 259
Low 1 1 2 4 9 4 1 3 122 3 4
Below cutoff 486 513 476 96 267 63 1037 421 615 60 235 444 33 273 629

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000432035   ⟹   ENSP00000455944
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl349,177,636 - 49,191,822 (-)Ensembl
RefSeq Acc Id: ENST00000443990
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl349,177,636 - 49,190,024 (-)Ensembl
RefSeq Acc Id: ENST00000545770   ⟹   ENSP00000454903
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl349,177,634 - 49,191,858 (-)Ensembl
RefSeq Acc Id: NM_001080528   ⟹   NP_001073997
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38349,177,634 - 49,191,858 (-)NCBI
GRCh37349,215,069 - 49,229,291 (-)NCBI
HuRef349,273,028 - 49,287,244 (-)NCBI
CHM1_1349,167,840 - 49,182,055 (-)NCBI
T2T-CHM13v2.0349,205,702 - 49,219,926 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011534015   ⟹   XP_011532317
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38349,177,634 - 49,191,858 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011534017   ⟹   XP_011532319
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38349,177,634 - 49,191,858 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054347547   ⟹   XP_054203522
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0349,205,607 - 49,219,926 (-)NCBI
RefSeq Acc Id: XM_054347548   ⟹   XP_054203523
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0349,205,607 - 49,219,926 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001073997   ⟸   NM_001080528
- UniProtKB: H3BNL1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011532319   ⟸   XM_011534017
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_011532317   ⟸   XM_011534015
- Peptide Label: isoform X1
- UniProtKB: H3BQU4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000454903   ⟸   ENST00000545770
RefSeq Acc Id: ENSP00000455944   ⟸   ENST00000432035
RefSeq Acc Id: XP_054203523   ⟸   XM_054347548
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054203522   ⟸   XM_054347547
- Peptide Label: isoform X1
- UniProtKB: H3BQU4 (UniProtKB/TrEMBL)
Protein Domains
Domain of unknown function with conserved HDNR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-H3BNL1-F1-model_v2 AlphaFold H3BNL1 1-204 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:44666 AgrOrtholog
COSMIC C3orf84 COSMIC
Ensembl Genes ENSG00000236980 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000432035 ENTREZGENE
  ENST00000432035.2 UniProtKB/TrEMBL
  ENST00000545770 ENTREZGENE
  ENST00000545770.7 UniProtKB/Swiss-Prot
GTEx ENSG00000236980 GTEx
HGNC ID HGNC:44666 ENTREZGENE
Human Proteome Map C3orf84 Human Proteome Map
InterPro HDNR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:646498 UniProtKB/Swiss-Prot
NCBI Gene C3orf84 ENTREZGENE
PANTHER CDNA SEQUENCE BC048562 UniProtKB/Swiss-Prot
  CDNA SEQUENCE BC048562 UniProtKB/Swiss-Prot
  CDNA SEQUENCE BC048562 UniProtKB/TrEMBL
  CDNA SEQUENCE BC048562 UniProtKB/TrEMBL
Pfam HDNR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA166123667 PharmGKB
UniProt CC084_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  H3BQU4 ENTREZGENE, UniProtKB/TrEMBL