IGKV1D-12 (immunoglobulin kappa variable 1D-12) - Rat Genome Database

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Gene: IGKV1D-12 (immunoglobulin kappa variable 1D-12) Homo sapiens
Analyze
No known orthologs.
Symbol: IGKV1D-12
Name: immunoglobulin kappa variable 1D-12
RGD ID: 1346046
HGNC Page HGNC:5746
Description: Predicted to be involved in immune response. Located in blood microparticle and extracellular exosome.
Type: gene (Ensembl: IG_V_gene)
RefSeq Status: VALIDATED
Previously known as: IGKV1D12; L19
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38290,159,860 - 90,160,335 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl290,159,840 - 90,160,335 (+)EnsemblGRCh38hg38GRCh38
GRCh37290,198,716 - 90,199,190 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36289,836,021 - 89,836,495 (+)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map2p11.2NCBI
HuRef288,507,317 - 88,507,853 (+)NCBIHuRef
CHM1_1290,128,027 - 90,128,502 (+)NCBICHM1_1
T2T-CHM13v2.0290,715,431 - 90,715,906 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
COVID-19  (HEP)

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. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients. Xiong Y, etal., Emerg Microbes Infect. 2020 Dec;9(1):761-770. doi: 10.1080/22221751.2020.1747363.
Additional References at PubMed
PMID:3927006   PMID:6778806   PMID:8223863   PMID:11298326   PMID:21873635   PMID:22516433   PMID:23376485   PMID:23533145   PMID:31180492  


Genomics

Variants

.
Variants in IGKV1D-12
1 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p11.2(chr2:89033009-90225016)x1 copy number loss See cases [RCV000134226] Chr2:89033009..90225016 [GRCh38]
Chr2:89332506..90263882 [GRCh37]
Chr2:89113621..89901187 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p12-11.2(chr2:77025216-90282666)x3 copy number gain See cases [RCV000134786] Chr2:77025216..90282666 [GRCh38]
Chr2:77252342..91619262 [GRCh37]
Chr2:77105850..90982989 [NCBI36]
Chr2:2p12-11.2		 pathogenic
GRCh38/hg38 2p11.2(chr2:88975768-91627653)x3 copy number gain See cases [RCV000135107] Chr2:88975768..91627653 [GRCh38]
Chr2:89275287..91815679 [GRCh37]
Chr2:89056402..91179406 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2-11.1(chr2:87098178-91884275)x3 copy number gain See cases [RCV000135666] Chr2:87098178..91884275 [GRCh38]
Chr2:87325301..92072301 [GRCh37]
Chr2:87178812..91436028 [NCBI36]
Chr2:2p11.2-11.1		 uncertain significance
GRCh38/hg38 2p11.2(chr2:89936685-90219425)x1 copy number loss See cases [RCV000136321] Chr2:89936685..90219425 [GRCh38]
Chr2:89975495..90258291 [GRCh37]
Chr2:89612800..89895596 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:87375475-90282666)x3 copy number gain See cases [RCV000137550] Chr2:87375475..90282666 [GRCh38]
Chr2:87602598..91619262 [GRCh37]
Chr2:87456109..90982989 [NCBI36]
Chr2:2p11.2		 uncertain significance
GRCh38/hg38 2p11.2(chr2:89023889-90225016)x3 copy number gain See cases [RCV000140120] Chr2:89023889..90225016 [GRCh38]
Chr2:89323386..90263882 [GRCh37]
Chr2:89104501..89901187 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:88988717-91627653)x3 copy number gain See cases [RCV000140130] Chr2:88988717..91627653 [GRCh38]
Chr2:89288236..91815679 [GRCh37]
Chr2:89069351..91179406 [NCBI36]
Chr2:2p11.2		 benign
GRCh38/hg38 2p11.2(chr2:89023889-91627653)x3 copy number gain See cases [RCV000141080] Chr2:89023889..91627653 [GRCh38]
Chr2:89323386..91815679 [GRCh37]
Chr2:89104501..91179406 [NCBI36]
Chr2:2p11.2		 benign
NC_000002.12:g.90160240G>A single nucleotide variant not provided [RCV003427104] Chr2:90160240 [GRCh38]
Chr2:90199095 [GRCh37]
Chr2:2p11.2		 likely benign
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:289
Count of miRNA genes:280
Interacting mature miRNAs:289
Transcripts:ENST00000390276
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 adipose tissue appendage
High
Medium 130 15 33 61 162 2 1 2 3 52 61 7 2
Low 601 497 168 116 713 31 116 12 29 18 130 512 85 116 56
Below cutoff 239 657 371 124 343 117 567 177 322 29 282 245 7 310 313

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000377032   ⟹   ENSP00000482464
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl290,159,840 - 90,160,335 (+)Ensembl
Protein Sequences
GenBank Protein CAA35167 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000482464.1
GenBank Protein P01611 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: ENSP00000482464   ⟸   ENST00000377032
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P01611-F1-model_v2 AlphaFold P01611 1-117 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5746 AgrOrtholog
COSMIC IGKV1D-12 COSMIC
Ensembl Genes ENSG00000278857 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000377032.5 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
GTEx ENSG00000278857 GTEx
HGNC ID HGNC:5746 ENTREZGENE
Human Proteome Map IGKV1D-12 Human Proteome Map
InterPro Ig-like_dom UniProtKB/Swiss-Prot
  Ig-like_dom_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  Ig_sub UniProtKB/Swiss-Prot
  Ig_V-set UniProtKB/Swiss-Prot
NCBI Gene IGKV1D-12 ENTREZGENE
PANTHER IMMUNOGLOBULIN KAPPA VARIABLE 1-12-RELATED UniProtKB/Swiss-Prot
  IMMUNOGLOBULIN LIGHT CHAIN UniProtKB/Swiss-Prot
Pfam V-set UniProtKB/Swiss-Prot
PharmGKB PA35328 PharmGKB
PROSITE IG_LIKE UniProtKB/Swiss-Prot
SMART IGv UniProtKB/Swiss-Prot
  SM00409 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot
UniProt KVD12_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary A0A0B4J2E7 UniProtKB/Swiss-Prot