CLEC4D (C-type lectin domain family 4 member D) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: CLEC4D (C-type lectin domain family 4 member D) Homo sapiens
Analyze
Symbol: CLEC4D
Name: C-type lectin domain family 4 member D
RGD ID: 1347298
HGNC Page HGNC:14554
Description: Enables D-mannose binding activity and pattern recognition receptor activity. Involved in antifungal innate immune response. Is active in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8; C-type lectin domain family 4, member D; C-type lectin receptor; C-type lectin superfamily member 8; C-type lectin-like receptor 6; CD368; CLEC-6; CLEC6; CLECSF8; DC-associated C-type lectin 3; Dectin 3; Dectin-3; dendritic cell-associated C-type lectin 3; macrophage C-type lectin; MCL; MGC40078; MPCL
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38128,513,503 - 8,531,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl128,509,475 - 8,522,366 (+)EnsemblGRCh38hg38GRCh38
GRCh37128,666,099 - 8,674,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,557,403 - 8,566,229 (+)NCBINCBI36Build 36hg18NCBI36
Build 34128,557,402 - 8,566,225NCBI
Celera1210,202,132 - 10,210,958 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef128,448,485 - 8,457,311 (+)NCBIHuRef
CHM1_1128,635,100 - 8,643,926 (+)NCBICHM1_1
T2T-CHM13v2.0128,496,932 - 8,515,063 (+)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

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
Additional References at PubMed
PMID:10508765   PMID:12477932   PMID:12945048   PMID:14971047   PMID:15368084   PMID:18029348   PMID:21873635   PMID:22689578   PMID:23911656   PMID:24101491   PMID:25910212   PMID:29616019  
PMID:32296183   PMID:32532809   PMID:34480018   PMID:34709727  


Genomics

Comparative Map Data
CLEC4D
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38128,513,503 - 8,531,696 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl128,509,475 - 8,522,366 (+)EnsemblGRCh38hg38GRCh38
GRCh37128,666,099 - 8,674,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,557,403 - 8,566,229 (+)NCBINCBI36Build 36hg18NCBI36
Build 34128,557,402 - 8,566,225NCBI
Celera1210,202,132 - 10,210,958 (+)NCBICelera
Cytogenetic Map12p13.31NCBI
HuRef128,448,485 - 8,457,311 (+)NCBIHuRef
CHM1_1128,635,100 - 8,643,926 (+)NCBICHM1_1
T2T-CHM13v2.0128,496,932 - 8,515,063 (+)NCBIT2T-CHM13v2.0
Clec4d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396123,239,066 - 123,252,227 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl6123,239,070 - 123,252,224 (+)EnsemblGRCm39 Ensembl
GRCm386123,262,107 - 123,275,268 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6123,262,111 - 123,275,265 (+)EnsemblGRCm38mm10GRCm38
MGSCv376123,212,125 - 123,225,286 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv366123,227,736 - 123,240,884 (+)NCBIMGSCv36mm8
Celera6125,059,667 - 125,072,919 (+)NCBICelera
Cytogenetic Map6F2NCBI
cM Map658.33NCBI
Clec4d
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84158,275,287 - 158,286,978 (+)NCBIGRCr8
mRatBN7.24156,589,591 - 156,599,279 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4156,589,792 - 156,598,848 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4162,841,890 - 162,851,041 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04158,624,772 - 158,633,925 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04157,270,184 - 157,279,333 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04156,253,084 - 156,264,766 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4156,253,079 - 156,264,769 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04223,269,999 - 223,281,665 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44159,883,556 - 159,892,609 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14160,128,491 - 160,137,545 (+)NCBI
Celera4145,381,212 - 145,388,954 (+)NCBICelera
Cytogenetic Map4q42NCBI
Clec4d
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554135,267,161 - 5,277,090 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554135,267,548 - 5,276,969 (-)NCBIChiLan1.0ChiLan1.0
CLEC4D
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21014,041,441 - 14,050,413 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11214,038,201 - 14,046,060 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0128,599,654 - 8,608,494 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1128,814,680 - 8,823,484 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl128,814,680 - 8,823,484 (+)Ensemblpanpan1.1panPan2
LOC611536
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12737,520,289 - 37,559,920 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2737,551,064 - 37,558,847 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha279,056,404 - 9,095,670 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02737,874,289 - 37,913,533 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2737,860,374 - 37,915,627 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12737,748,924 - 37,788,104 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02737,790,476 - 37,829,811 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0278,543,144 - 8,582,370 (-)NCBIUU_Cfam_GSD_1.0
Clec4d
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494599,887,289 - 99,896,017 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936858303,639 - 312,083 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936858303,639 - 312,092 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110258710
(Sus scrofa - pig)		 No map positions available.
CLEC4D
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1118,294,999 - 8,303,866 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666089393,835 - 402,286 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in CLEC4D
24 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p13.33-11.22(chr12:121055-28415184)x1 copy number loss See cases [RCV000052776] Chr12:121055..28415184 [GRCh38]
Chr12:282465..28568117 [GRCh37]
Chr12:100482..28459384 [NCBI36]
Chr12:12p13.33-11.22		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
NM_080387.4(CLEC4D):c.121+894A>C single nucleotide variant Lung cancer [RCV000097501] Chr12:8516222 [GRCh38]
Chr12:8668818 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-12.3(chr12:2871741-14987348)x3 copy number gain See cases [RCV000137694] Chr12:2871741..14987348 [GRCh38]
Chr12:2980907..15140282 [GRCh37]
Chr12:2851168..15031549 [NCBI36]
Chr12:12p13.33-12.3		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh38/hg38 12p13.31(chr12:8455575-8623334)x1 copy number loss See cases [RCV000141172] Chr12:8455575..8623334 [GRCh38]
Chr12:8608171..8775930 [GRCh37]
Chr12:8499438..8667197 [NCBI36]
Chr12:12p13.31		 likely benign
GRCh38/hg38 12p13.33-12.2(chr12:1258274-20657577)x3 copy number gain See cases [RCV000141905] Chr12:1258274..20657577 [GRCh38]
Chr12:1367440..20810511 [GRCh37]
Chr12:1237701..20701778 [NCBI36]
Chr12:12p13.33-12.2		 pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:148034-34178799)x4 copy number gain See cases [RCV000240164] Chr12:148034..34178799 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:89061-34178799)x3 copy number gain See cases [RCV000240487] Chr12:89061..34178799 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NC_000012.12:g.(1_3750000)_(5250000_9000000)del deletion Tumoral calcinosis, hyperphosphatemic, familial, 1 [RCV000758697] Chr12:3750000..5250000 [GRCh38]
Chr12:12p13.33-13.31		 pathogenic|not provided
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301)x3 copy number gain See cases [RCV000449191] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865)x3 copy number gain See cases [RCV000449287] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain See cases [RCV000447551] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-12.2(chr12:173786-20026080)x3 copy number gain See cases [RCV000446050] Chr12:173786..20026080 [GRCh37]
Chr12:12p13.33-12.2		 pathogenic
GRCh37/hg19 12p13.31(chr12:8608171-8765397) copy number loss See cases [RCV000447204] Chr12:8608171..8765397 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:189578-34756150) copy number gain See cases [RCV000446017] Chr12:189578..34756150 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NM_080387.5(CLEC4D):c.94A>G (p.Ser32Gly) single nucleotide variant not provided [RCV004707271]|not specified [RCV000454730] Chr12:8515301 [GRCh38]
Chr12:8667897 [GRCh37]
Chr12:12p13.31		 benign
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 copy number gain See cases [RCV000511580] Chr12:565369..34835837 [GRCh37]
Chr12:12p13.33-11.1		 likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-13.2(chr12:173786-11677456)x3 copy number gain See cases [RCV000510853] Chr12:173786..11677456 [GRCh37]
Chr12:12p13.33-13.2		 pathogenic
GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 copy number gain See cases [RCV000510961] Chr12:173786..28219229 [GRCh37]
Chr12:12p13.33-11.22		 pathogenic
NM_080387.5(CLEC4D):c.293C>A (p.Pro98His) single nucleotide variant not specified [RCV004297829] Chr12:8519069 [GRCh38]
Chr12:8671665 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh37/hg19 12p13.33-q11(chr12:173786-37869107)x3 copy number gain not provided [RCV000683480] Chr12:173786..37869107 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x2,3 copy number gain not provided [RCV000683478] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain not provided [RCV000683479] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33		 pathogenic
GRCh37/hg19 12p13.31(chr12:8029351-8705395)x3 copy number gain not provided [RCV000737754] Chr12:8029351..8705395 [GRCh37]
Chr12:12p13.31		 benign
GRCh37/hg19 12p13.33-11.21(chr12:191619-31733044)x3 copy number gain not provided [RCV000750245] Chr12:191619..31733044 [GRCh37]
Chr12:12p13.33-11.21		 pathogenic
GRCh37/hg19 12p13.31(chr12:6911437-9381254)x3 copy number gain not provided [RCV000750277] Chr12:6911437..9381254 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.177G>A (p.Glu59=) single nucleotide variant not provided [RCV001703368] Chr12:8518219 [GRCh38]
Chr12:8670815 [GRCh37]
Chr12:12p13.31		 likely benign
GRCh37/hg19 12p13.33-q11(chr12:274676-37869301)x4 copy number gain not provided [RCV001006470] Chr12:274676..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-12.3(chr12:189216-15001420) copy number gain not provided [RCV000767817] Chr12:189216..15001420 [GRCh37]
Chr12:12p13.33-12.3		 pathogenic
NC_000012.11:g.(?_6945914)_(9027627_?)dup duplication Temtamy syndrome [RCV000816630] Chr12:6945914..9027627 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:173786-34496628)x3 copy number gain not provided [RCV000847209] Chr12:173786..34496628 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NM_080387.5(CLEC4D):c.137T>C (p.Phe46Ser) single nucleotide variant not specified [RCV004301570] Chr12:8518179 [GRCh38]
Chr12:8670775 [GRCh37]
Chr12:12p13.31		 uncertain significance
NC_000012.11:g.(?_4368352)_(9027607_?)dup duplication Lymphoproliferative syndrome 2 [RCV003105682] Chr12:4368352..9027607 [GRCh37]
Chr12:12p13.32-13.31		 uncertain significance
NC_000012.12:g.(?_8456112)_(8612767_?)del deletion Hyper-IgM syndrome type 2 [RCV001031871] Chr12:8608708..8765363 [GRCh37]
Chr12:12p13.31		 pathogenic
NC_000012.11:g.(?_6945914)_(9027627_?)dup duplication Developmental and epileptic encephalopathy, 21 [RCV001325295]|Klippel-Feil syndrome 3, autosomal dominant [RCV001301079]|Temtamy syndrome [RCV000816630]|not provided [RCV001859243] Chr12:6945914..9027627 [GRCh37]
Chr12:12p13.31		 uncertain significance|no classifications from unflagged records
NC_000012.11:g.(?_6438478)_(8756953_?)dup duplication not provided [RCV001970781] Chr12:6438478..8756953 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865) copy number gain not specified [RCV002052955] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1		 pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301) copy number gain not specified [RCV002052958] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837) copy number gain not specified [RCV002052957] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NC_000012.11:g.(?_6438478)_(9027607_?)dup duplication not provided [RCV001943267] Chr12:6438478..9027607 [GRCh37]
Chr12:12p13.31		 uncertain significance
NC_000012.11:g.(?_6978008)_(9010204_?)dup duplication Peroxisome biogenesis disorder 2B [RCV001877402] Chr12:6978008..9010204 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.602T>C (p.Phe201Ser) single nucleotide variant not specified [RCV004211007] Chr12:8521225 [GRCh38]
Chr12:8673821 [GRCh37]
Chr12:12p13.31		 likely benign
NM_080387.5(CLEC4D):c.110C>A (p.Ala37Glu) single nucleotide variant not specified [RCV004082323] Chr12:8515317 [GRCh38]
Chr12:8667913 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.479C>T (p.Thr160Met) single nucleotide variant not specified [RCV004109614] Chr12:8520320 [GRCh38]
Chr12:8672916 [GRCh37]
Chr12:12p13.31		 likely benign
NM_080387.5(CLEC4D):c.596G>T (p.Cys199Phe) single nucleotide variant not specified [RCV004077363] Chr12:8521219 [GRCh38]
Chr12:8673815 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.330G>C (p.Arg110Ser) single nucleotide variant not specified [RCV004105192] Chr12:8519106 [GRCh38]
Chr12:8671702 [GRCh37]
Chr12:12p13.31		 uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:176047-34179852)x4 copy number gain Pallister-Killian syndrome [RCV003154827] Chr12:176047..34179852 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NM_080387.5(CLEC4D):c.197G>T (p.Cys66Phe) single nucleotide variant not specified [RCV004275803] Chr12:8518239 [GRCh38]
Chr12:8670835 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.247T>G (p.Cys83Gly) single nucleotide variant not specified [RCV004258585] Chr12:8519023 [GRCh38]
Chr12:8671619 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.616A>G (p.Ile206Val) single nucleotide variant not specified [RCV004339336] Chr12:8521239 [GRCh38]
Chr12:8673835 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.218T>C (p.Leu73Pro) single nucleotide variant not specified [RCV004338540] Chr12:8518260 [GRCh38]
Chr12:8670856 [GRCh37]
Chr12:12p13.31		 uncertain significance
Single allele duplication not provided [RCV003448692] Chr12:188053..34856694 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835641)x3 copy number gain not specified [RCV003986979] Chr12:173786..34835641 [GRCh37]
Chr12:12p13.33-11.1		 pathogenic
NM_080387.5(CLEC4D):c.458A>G (p.Gln153Arg) single nucleotide variant not specified [RCV004437000] Chr12:8520299 [GRCh38]
Chr12:8672895 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.170A>G (p.Lys57Arg) single nucleotide variant not specified [RCV004436994] Chr12:8518212 [GRCh38]
Chr12:8670808 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.510T>A (p.His170Gln) single nucleotide variant not specified [RCV004437002] Chr12:8521133 [GRCh38]
Chr12:8673729 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.199A>G (p.Ile67Val) single nucleotide variant not specified [RCV004436995] Chr12:8518241 [GRCh38]
Chr12:8670837 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.311C>T (p.Thr104Met) single nucleotide variant not specified [RCV004436996] Chr12:8519087 [GRCh38]
Chr12:8671683 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.376G>A (p.Ala126Thr) single nucleotide variant not specified [RCV004436997] Chr12:8519152 [GRCh38]
Chr12:8671748 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.412C>T (p.Arg138Trp) single nucleotide variant not specified [RCV004436999] Chr12:8520253 [GRCh38]
Chr12:8672849 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.509A>G (p.His170Arg) single nucleotide variant not specified [RCV004437001] Chr12:8521132 [GRCh38]
Chr12:8673728 [GRCh37]
Chr12:12p13.31		 uncertain significance
NM_080387.5(CLEC4D):c.614G>C (p.Arg205Thr) single nucleotide variant not specified [RCV004612989] Chr12:8521237 [GRCh38]
Chr12:8673833 [GRCh37]
Chr12:12p13.31		 uncertain significance
NC_000012.11:g.(?_7053285)_(9027607_?)del deletion Developmental and epileptic encephalopathy, 21 [RCV004578381]|Peroxisome biogenesis disorder 2B [RCV004578380] Chr12:7053285..9027607 [GRCh37]
Chr12:12p13.31		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:476
Count of miRNA genes:405
Interacting mature miRNAs:433
Transcripts:ENST00000299665, ENST00000382064
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.

Markers in Region
MARC_4325-4326:991938466:1  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37128,665,009 - 8,665,131UniSTSGRCh37
GRCh371756,423,651 - 56,424,934UniSTSGRCh37
Build 36128,556,276 - 8,556,398RGDNCBI36
Celera1752,885,437 - 52,886,722UniSTS
Celera1210,201,005 - 10,201,127RGD
HuRef128,447,358 - 8,447,480UniSTS
HuRef1751,784,268 - 51,785,553UniSTS
MARC_3557-3558:966881413:1  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37128,665,079 - 8,665,199UniSTSGRCh37
Build 36128,556,346 - 8,556,466RGDNCBI36
Celera1210,201,075 - 10,201,195RGD
HuRef128,447,428 - 8,447,548UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
1170 1846 2225 2019 3183 1402 1851 2 461 1531 326 1711 5830 5589 9 2471 657 1396 1312 135

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_080387 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011520632 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011520633 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047428771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047428772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054371926 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054371927 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054371928 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC092746 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF411850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK314071 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY115592 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY297446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY486482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY486483 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC032313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BI909298 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068266 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENST00000299665   ⟹   ENSP00000299665
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl128,513,503 - 8,522,366 (+)Ensembl
Ensembl Acc Id: ENST00000382064   ⟹   ENSP00000371496
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl128,509,475 - 8,520,273 (+)Ensembl
RefSeq Acc Id: NM_080387   ⟹   NP_525126
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38128,513,503 - 8,522,366 (+)NCBI
GRCh37128,666,136 - 8,674,962 (+)RGD
Build 36128,557,403 - 8,566,229 (+)NCBI Archive
Celera1210,202,132 - 10,210,958 (+)RGD
HuRef128,448,485 - 8,457,311 (+)RGD
CHM1_1128,635,100 - 8,643,926 (+)NCBI
T2T-CHM13v2.0128,496,962 - 8,505,825 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011520632   ⟹   XP_011518934
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38128,513,503 - 8,522,366 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047428771   ⟹   XP_047284727
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38128,513,503 - 8,531,696 (+)NCBI
RefSeq Acc Id: XM_047428772   ⟹   XP_047284728
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38128,513,503 - 8,531,696 (+)NCBI
RefSeq Acc Id: XM_054371926   ⟹   XP_054227901
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0128,496,932 - 8,505,825 (+)NCBI
RefSeq Acc Id: XM_054371927   ⟹   XP_054227902
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0128,496,962 - 8,515,063 (+)NCBI
RefSeq Acc Id: XM_054371928   ⟹   XP_054227903
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0128,496,962 - 8,515,063 (+)NCBI
RefSeq Acc Id: NP_525126   ⟸   NM_080387
- UniProtKB: Q8N5J5 (UniProtKB/Swiss-Prot),   Q8WXI8 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011518934   ⟸   XM_011520632
- Peptide Label: isoform X1
- UniProtKB: Q8N5J5 (UniProtKB/Swiss-Prot),   Q8WXI8 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000299665   ⟸   ENST00000299665
Ensembl Acc Id: ENSP00000371496   ⟸   ENST00000382064
RefSeq Acc Id: XP_047284728   ⟸   XM_047428772
- Peptide Label: isoform X3
RefSeq Acc Id: XP_047284727   ⟸   XM_047428771
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054227901   ⟸   XM_054371926
- Peptide Label: isoform X1
- UniProtKB: Q8WXI8 (UniProtKB/Swiss-Prot),   Q8N5J5 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054227903   ⟸   XM_054371928
- Peptide Label: isoform X3
RefSeq Acc Id: XP_054227902   ⟸   XM_054371927
- Peptide Label: isoform X2
Protein Domains
C-type lectin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8WXI8-F1-model_v2 AlphaFold Q8WXI8 1-215 view protein structure

Promoters
RGD ID:7223075
Promoter ID:EPDNEW_H17282
Type:initiation region
Name:CLEC4D_1
Description:C-type lectin domain family 4 member D
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38128,513,538 - 8,513,598EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:14554 AgrOrtholog
COSMIC CLEC4D COSMIC
Ensembl Genes ENSG00000166527 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000299665 ENTREZGENE
  ENST00000299665.3 UniProtKB/Swiss-Prot
  ENST00000382064.6 UniProtKB/TrEMBL
Gene3D-CATH 3.10.100.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000166527 GTEx
HGNC ID HGNC:14554 ENTREZGENE
Human Proteome Map CLEC4D Human Proteome Map
InterPro C-type_lectin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_lectin-like/link_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  C-type_Lectin_Receptor_IMM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CD209-like_CTLD UniProtKB/Swiss-Prot
  CTDL_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:338339 UniProtKB/Swiss-Prot
NCBI Gene 338339 ENTREZGENE
OMIM 609964 OMIM
PANTHER CD209 ANTIGEN-LIKE PROTEIN C-LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  KILLER CELL LECTIN-LIKE RECEPTOR SUBFAMILY F MEMBER 2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lectin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134916109 PharmGKB
PROSITE C_TYPE_LECTIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CLECT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF56436 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6NHA5_HUMAN UniProtKB/TrEMBL
  CLC4D_HUMAN UniProtKB/Swiss-Prot
  Q8N5J5 ENTREZGENE
  Q8WXI8 ENTREZGENE
UniProt Secondary Q8N5J5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-12-22 CLEC4D  C-type lectin domain family 4 member D  CLEC4D  C-type lectin domain family 4, member D  Symbol and/or name change 5135510 APPROVED