RAB6D (RAB6D, member RAS oncogene family) - Rat Genome Database

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Gene: RAB6D (RAB6D, member RAS oncogene family) Homo sapiens
Analyze
Symbol: RAB6D
Name: RAB6D, member RAS oncogene family
RGD ID: 13440557
HGNC Page HGNC:30272
Description: Predicted to enable GTPase activity. Predicted to be involved in Golgi vesicle transport; intracellular protein transport; and retrograde transport, endosome to Golgi. Located in Golgi apparatus.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: rab6-like protein WTH3DI; RAB6C-like; RAB6CL; ras-related protein Rab-6D; WTH3DI
RGD Orthologs
Bonobo
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
GRCh382131,360,492 - 131,364,168 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2131,360,492 - 131,364,168 (-)EnsemblGRCh38hg38GRCh38
GRCh372132,118,065 - 132,121,741 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362131,834,535 - 131,838,201 (-)NCBINCBI36Build 36hg18NCBI36
Celera2125,841,288 - 125,844,954 (-)NCBICelera
Cytogenetic Map2q21.1NCBI
HuRef2124,112,169 - 124,115,861 (-)NCBIHuRef
CHM1_12132,121,682 - 132,125,350 (-)NCBICHM1_1
T2T-CHM13v2.02131,795,201 - 131,798,903 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:9847074   PMID:16344560   PMID:16923123   PMID:21873635   PMID:31871319   PMID:32552912   PMID:37616343  


Genomics

Comparative Map Data
RAB6D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382131,360,492 - 131,364,168 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2131,360,492 - 131,364,168 (-)EnsemblGRCh38hg38GRCh38
GRCh372132,118,065 - 132,121,741 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362131,834,535 - 131,838,201 (-)NCBINCBI36Build 36hg18NCBI36
Celera2125,841,288 - 125,844,954 (-)NCBICelera
Cytogenetic Map2q21.1NCBI
HuRef2124,112,169 - 124,115,861 (-)NCBIHuRef
CHM1_12132,121,682 - 132,125,350 (-)NCBICHM1_1
T2T-CHM13v2.02131,795,201 - 131,798,903 (-)NCBIT2T-CHM13v2.0
RAB6D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21344,269,515 - 44,270,464 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B44,284,487 - 44,285,436 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B29,009,755 - 29,012,600 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B130,642,867 - 130,644,070 (+)NCBIpanpan1.1PanPan1.1panPan2


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2q21.1(chr2:130743933-131451535)x1 copy number loss See cases [RCV000137148] Chr2:130743933..131451535 [GRCh38]
Chr2:131501506..132209108 [GRCh37]
Chr2:131217976..131925578 [NCBI36]
Chr2:2q21.1
uncertain significance
GRCh38/hg38 2q21.1(chr2:131337384-131605323)x1 copy number loss See cases [RCV000139227] Chr2:131337384..131605323 [GRCh38]
Chr2:132094957..132362896 [GRCh37]
Chr2:131811427..132079366 [NCBI36]
Chr2:2q21.1
likely benign|uncertain significance
GRCh38/hg38 2q21.1(chr2:131340404-131643336)x1 copy number loss See cases [RCV000139536] Chr2:131340404..131643336 [GRCh38]
Chr2:132097977..132400909 [GRCh37]
Chr2:131814447..132117379 [NCBI36]
Chr2:2q21.1
likely benign
GRCh38/hg38 2q21.1(chr2:131337384-131619715)x1 copy number loss See cases [RCV000140823] Chr2:131337384..131619715 [GRCh38]
Chr2:132094957..132377288 [GRCh37]
Chr2:131811427..132093758 [NCBI36]
Chr2:2q21.1
likely benign|uncertain significance
GRCh38/hg38 2q21.1(chr2:131271331-131497222)x0 copy number loss See cases [RCV000141774] Chr2:131271331..131497222 [GRCh38]
Chr2:132028904..132254795 [GRCh37]
Chr2:131745374..131971265 [NCBI36]
Chr2:2q21.1
likely benign
GRCh38/hg38 2q21.1(chr2:130720374-131388759)x3 copy number gain See cases [RCV000143474] Chr2:130720374..131388759 [GRCh38]
Chr2:131477947..132146332 [GRCh37]
Chr2:131194417..131862802 [NCBI36]
Chr2:2q21.1
likely benign
GRCh38/hg38 2q14.1-21.3(chr2:118086324-134964738)x1 copy number loss See cases [RCV000054058] Chr2:118086324..134964738 [GRCh38]
Chr2:118843900..135722308 [GRCh37]
Chr2:118560370..135438778 [NCBI36]
Chr2:2q14.1-21.3
pathogenic
GRCh38/hg38 2q14.3-22.1(chr2:123445762-140592538)x1 copy number loss See cases [RCV000136714] Chr2:123445762..140592538 [GRCh38]
Chr2:124203338..141350107 [GRCh37]
Chr2:123919808..141066577 [NCBI36]
Chr2:2q14.3-22.1
pathogenic
GRCh38/hg38 2q21.1-21.2(chr2:131100857-132436431)x3 copy number gain See cases [RCV000141447] Chr2:131100857..132436431 [GRCh38]
Chr2:131858430..133194004 [GRCh37]
Chr2:131574900..132910474 [NCBI36]
Chr2:2q21.1-21.2
uncertain significance
GRCh38/hg38 2q21.1-21.2(chr2:131291207-132406186)x3 copy number gain See cases [RCV000142215] Chr2:131291207..132406186 [GRCh38]
Chr2:132048780..133163759 [GRCh37]
Chr2:131765250..132880229 [NCBI36]
Chr2:2q21.1-21.2
likely benign|uncertain significance
GRCh38/hg38 2q21.1(chr2:131310498-131508954)x3 copy number gain See cases [RCV000135111] Chr2:131310498..131508954 [GRCh38]
Chr2:132068071..132266527 [GRCh37]
Chr2:131784541..131982997 [NCBI36]
Chr2:2q21.1
benign
GRCh38/hg38 2q21.1(chr2:130743933-131549753)x1 copy number loss See cases [RCV000137130] Chr2:130743933..131549753 [GRCh38]
Chr2:131501506..132307326 [GRCh37]
Chr2:131217976..132023796 [NCBI36]
Chr2:2q21.1
likely pathogenic|uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:70
Count of miRNA genes:68
Interacting mature miRNAs:68
Transcripts:ENST00000484914, ENST00000535957
Prediction methods:Microtar, 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 adipose tissue appendage
High
Medium 1 1 5
Low 494 24 39 19 112 19 20 76 1240 39 629 35 1 5 11
Below cutoff 1767 2396 1310 354 1065 220 3614 1798 2289 262 645 1265 137 1089 2438

Sequence


RefSeq Acc Id: ENST00000623617   ⟹   ENSP00000490038
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2131,360,492 - 131,364,168 (-)Ensembl
RefSeq Acc Id: NM_001077637   ⟹   NP_001071105
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382131,360,492 - 131,364,168 (-)NCBI
CHM1_12132,121,682 - 132,125,350 (-)NCBI
T2T-CHM13v2.02131,795,201 - 131,798,903 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001071105 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAX93251 (Get FASTA)   NCBI Sequence Viewer  
  AAY33873 (Get FASTA)   NCBI Sequence Viewer  
  BAF02860 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000490038
  ENSP00000490038.1
GenBank Protein Q53S08 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001071105   ⟸   NM_001077637
- UniProtKB: Q53S08 (UniProtKB/TrEMBL),   Q53ET8 (UniProtKB/TrEMBL),   Q6FGX3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000490038   ⟸   ENST00000623617

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q53S08-F1-model_v2 AlphaFold Q53S08 1-254 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:30272 AgrOrtholog
COSMIC RAB6D COSMIC
Ensembl Genes ENSG00000233087 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000623617 ENTREZGENE
  ENST00000623617.3 UniProtKB/Swiss-Prot
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000233087 GTEx
HGNC ID HGNC:30272 ENTREZGENE
Human Proteome Map RAB6D Human Proteome Map
InterPro P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:150786 UniProtKB/Swiss-Prot
NCBI Gene RAB6D ENTREZGENE
PANTHER RAB6A, MEMBER RAS ONCOGENE FAMILY UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAS-RELATED PROTEIN RAB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ras UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA166181614 PharmGKB
PRINTS RASTRNSFRMNG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE RAB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  RHO UniProtKB/TrEMBL
SMART RAB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RHO UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP P-loop containing nucleoside triphosphate hydrolases UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt Q53ET8 ENTREZGENE
  Q53S08 ENTREZGENE
  Q6FGX3 ENTREZGENE, UniProtKB/TrEMBL
  RAB6D_HUMAN UniProtKB/Swiss-Prot