CLIC3 (chloride intracellular channel 3) - 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   new 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
Gene: CLIC3 (chloride intracellular channel 3) Homo sapiens
Analyze
Symbol: CLIC3
Name: chloride intracellular channel 3
RGD ID: 1316330
HGNC Page HGNC:2064
Description: Enables chloride channel activity. Involved in chloride transport. Located in cytoplasm and nuclear body.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: chloride intracellular channel protein 3
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
GRCh389136,994,608 - 136,996,568 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,994,608 - 136,996,568 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,889,060 - 139,891,020 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,008,881 - 139,010,845 (-)NCBINCBI36Build 36hg18NCBI36
Build 349137,164,896 - 137,166,861NCBI
Celera9110,401,370 - 110,403,334 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,348,166 - 109,350,130 (-)NCBIHuRef
CHM1_19140,037,817 - 140,039,781 (-)NCBICHM1_1
T2T-CHM13v2.09149,229,019 - 149,230,979 (-)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

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Seizure  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9139710   PMID:9880541   PMID:11563969   PMID:12477932   PMID:15489334   PMID:17027078   PMID:17207965   PMID:18029348   PMID:19056867   PMID:20146363   PMID:21044950   PMID:21832049  
PMID:21873635   PMID:22795578   PMID:23376485   PMID:23403292   PMID:25015290   PMID:25416956   PMID:26344197   PMID:26445368   PMID:28198360   PMID:28514442   PMID:30575818   PMID:31515488  
PMID:32066374   PMID:32296183   PMID:33961781   PMID:34766585   PMID:35238065   PMID:35831314   PMID:38182571  


Genomics

Comparative Map Data
CLIC3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389136,994,608 - 136,996,568 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9136,994,608 - 136,996,568 (-)EnsemblGRCh38hg38GRCh38
GRCh379139,889,060 - 139,891,020 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369139,008,881 - 139,010,845 (-)NCBINCBI36Build 36hg18NCBI36
Build 349137,164,896 - 137,166,861NCBI
Celera9110,401,370 - 110,403,334 (-)NCBICelera
Cytogenetic Map9q34.3NCBI
HuRef9109,348,166 - 109,350,130 (-)NCBIHuRef
CHM1_19140,037,817 - 140,039,781 (-)NCBICHM1_1
T2T-CHM13v2.09149,229,019 - 149,230,979 (-)NCBIT2T-CHM13v2.0
Clic3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39225,346,855 - 25,348,789 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl225,346,850 - 25,348,788 (+)EnsemblGRCm39 Ensembl
GRCm38225,456,843 - 25,458,777 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl225,456,838 - 25,458,776 (+)EnsemblGRCm38mm10GRCm38
MGSCv37225,312,363 - 25,314,292 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36225,278,852 - 25,280,781 (+)NCBIMGSCv36mm8
Celera225,184,332 - 25,186,261 (+)NCBICelera
Cytogenetic Map2A3NCBI
cM Map217.27NCBI
Clic3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8328,670,176 - 28,672,166 (+)NCBIGRCr8
mRatBN7.238,271,416 - 8,274,023 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl38,272,097 - 8,274,018 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx311,377,185 - 11,379,096 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0319,963,409 - 19,965,320 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0318,153,257 - 18,155,168 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.032,675,732 - 2,678,248 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl32,676,296 - 2,680,565 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.032,657,743 - 2,659,664 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.433,622,894 - 3,624,805 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.133,623,545 - 3,624,807 (+)NCBI
Celera33,097,212 - 3,099,123 (+)NCBICelera
Cytogenetic Map3p13NCBI
Clic3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555135,020,144 - 5,021,936 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555135,020,105 - 5,022,000 (-)NCBIChiLan1.0ChiLan1.0
CLIC3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2112,401,954 - 2,404,212 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan192,404,606 - 2,406,683 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09108,054,934 - 108,057,100 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19137,023,465 - 137,025,522 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9137,023,505 - 137,025,361 (-)Ensemblpanpan1.1panPan2
CLIC3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1948,634,061 - 48,637,083 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl948,634,878 - 48,637,015 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha947,848,449 - 47,850,740 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0949,512,882 - 49,515,171 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl949,512,968 - 49,515,955 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1948,289,095 - 48,291,384 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0948,587,812 - 48,590,101 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0948,635,170 - 48,637,460 (+)NCBIUU_Cfam_GSD_1.0
Clic3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947202,424,519 - 202,427,338 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936669948,667 - 950,539 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936669947,743 - 950,539 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLIC3
(Sus scrofa - pig)		 No map positions available.
CLIC3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1121,198,192 - 1,200,296 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl121,198,387 - 1,200,246 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660584,101,042 - 4,103,201 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clic3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624760911,145 - 912,951 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624760911,124 - 912,922 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CLIC3
14 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 9q34.3(chr9:136323974-138014606)x1 copy number loss See cases [RCV000050344] Chr9:136323974..138014606 [GRCh38]
Chr9:139218428..140909058 [GRCh37]
Chr9:138338249..140028879 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000050348] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:122792658-138124532)x3 copy number gain See cases [RCV000051040] Chr9:122792658..138124532 [GRCh38]
Chr9:125554937..141018984 [GRCh37]
Chr9:124594758..140138805 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136323974-138124532)x1 copy number loss See cases [RCV000051116] Chr9:136323974..138124532 [GRCh38]
Chr9:139218428..141018984 [GRCh37]
Chr9:138338249..140138805 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121112395-138075224)x3 copy number gain See cases [RCV000051009] Chr9:121112395..138075224 [GRCh38]
Chr9:123874673..140969676 [GRCh37]
Chr9:122914494..140089497 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134428674-138154922)x1 copy number loss See cases [RCV000052936] Chr9:134428674..138154922 [GRCh38]
Chr9:137320520..141049374 [GRCh37]
Chr9:136460341..140169195 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135452016-137613738)x1 copy number loss See cases [RCV000052937] Chr9:135452016..137613738 [GRCh38]
Chr9:138343862..140508190 [GRCh37]
Chr9:137483683..139628011 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136015976-138124532)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052938]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052938]|See cases [RCV000052938] Chr9:136015976..138124532 [GRCh38]
Chr9:138907822..141018984 [GRCh37]
Chr9:138047643..140138805 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136926575-138114463)x1 copy number loss See cases [RCV000052940] Chr9:136926575..138114463 [GRCh38]
Chr9:139821027..141008915 [GRCh37]
Chr9:138940848..140128736 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124532)x3 copy number gain See cases [RCV000053745] Chr9:193412..138124532 [GRCh38]
Chr9:204193..141018984 [GRCh37]
Chr9:194193..140138805 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053748]|See cases [RCV000053748] Chr9:193412..138179445 [GRCh38]
Chr9:266045..141073897 [GRCh37]
Chr9:256045..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:134174698-138138735)x3 copy number gain See cases [RCV000053814] Chr9:134174698..138138735 [GRCh38]
Chr9:137091194..141033187 [GRCh37]
Chr9:136029641..140153008 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138114463)x3 copy number gain See cases [RCV000053746] Chr9:193412..138114463 [GRCh38]
Chr9:214367..141008915 [GRCh37]
Chr9:204367..140128736 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121586837-138179445)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053776]|See cases [RCV000053776] Chr9:121586837..138179445 [GRCh38]
Chr9:124349116..141073897 [GRCh37]
Chr9:123388937..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:204193-138179445) copy number gain See cases [RCV000133791] Chr9:204193..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:130513207-138124532)x3 copy number gain See cases [RCV000133778] Chr9:130513207..138124532 [GRCh38]
Chr9:133388594..141018984 [GRCh37]
Chr9:132378415..140138805 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q34.11-34.3(chr9:129068560-138179445)x3 copy number gain See cases [RCV000134916] Chr9:129068560..138179445 [GRCh38]
Chr9:131830839..141073897 [GRCh37]
Chr9:130870660..140193718 [NCBI36]
Chr9:9q34.11-34.3		 pathogenic
GRCh38/hg38 9q33.2-34.3(chr9:121073102-138179445)x3 copy number gain See cases [RCV000134920] Chr9:121073102..138179445 [GRCh38]
Chr9:123835380..141073897 [GRCh37]
Chr9:122875201..140193718 [NCBI36]
Chr9:9q33.2-34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132986903-138114463)x3 copy number gain See cases [RCV000136790] Chr9:132986903..138114463 [GRCh38]
Chr9:135862290..141008915 [GRCh37]
Chr9:134852111..140128736 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133504071-138159073)x3 copy number gain See cases [RCV000137825] Chr9:133504071..138159073 [GRCh38]
Chr9:136324358..141053525 [GRCh37]
Chr9:135314179..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138124524)x3 copy number gain See cases [RCV000138783] Chr9:193412..138124524 [GRCh38]
Chr9:204090..141018976 [GRCh37]
Chr9:194090..140138797 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000138962] Chr9:193412..138159073 [GRCh38]
Chr9:204104..141053525 [GRCh37]
Chr9:194104..140173346 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic|conflicting data from submitters
GRCh38/hg38 9p11.2-q34.3(chr9:193412-138159073)x3 copy number gain See cases [RCV000139207] Chr9:193412..138159073 [GRCh38]
Chr9:68420641..141053525 [GRCh37]
Chr9:67910461..140173346 [NCBI36]
Chr9:9p11.2-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133996227-138124524)x3 copy number gain See cases [RCV000139807] Chr9:133996227..138124524 [GRCh38]
Chr9:136861349..141018976 [GRCh37]
Chr9:135851170..140138797 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203861-138125937)x3 copy number gain See cases [RCV000141876] Chr9:203861..138125937 [GRCh38]
Chr9:203861..141020389 [GRCh37]
Chr9:193861..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.2-34.3(chr9:133918071-138159073)x3 copy number gain See cases [RCV000142955] Chr9:133918071..138159073 [GRCh38]
Chr9:136783193..141053525 [GRCh37]
Chr9:135773014..140173346 [NCBI36]
Chr9:9q34.2-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136877772-138124524)x1 copy number loss See cases [RCV000142978] Chr9:136877772..138124524 [GRCh38]
Chr9:139772224..141018976 [GRCh37]
Chr9:138892045..140138797 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9q34.13-34.3(chr9:132386553-138059695)x3 copy number gain See cases [RCV000142636] Chr9:132386553..138059695 [GRCh38]
Chr9:135261940..140954147 [GRCh37]
Chr9:134251761..140073968 [NCBI36]
Chr9:9q34.13-34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:135704780-138125937)x4 copy number gain See cases [RCV000143394] Chr9:135704780..138125937 [GRCh38]
Chr9:138596626..141020389 [GRCh37]
Chr9:137736447..140140210 [NCBI36]
Chr9:9q34.3		 likely pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:203862-138125937)x3 copy number gain See cases [RCV000143476] Chr9:203862..138125937 [GRCh38]
Chr9:203862..141020389 [GRCh37]
Chr9:193862..140140210 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh38/hg38 9q34.3(chr9:136323974-138014606)x1 copy number loss See cases [RCV000148284] Chr9:136323974..138014606 [GRCh38]
Chr9:139218428..140909058 [GRCh37]
Chr9:138338249..140028879 [NCBI36]
Chr9:9q34.3		 pathogenic
GRCh38/hg38 9p24.3-q34.3(chr9:193412-138179445)x3 copy number gain See cases [RCV000148113] Chr9:193412..138179445 [GRCh38]
Chr9:204193..141073897 [GRCh37]
Chr9:194193..140193718 [NCBI36]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:163131-141122114)x3 copy number gain See cases [RCV000240081] Chr9:163131..141122114 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:62525-141006407) copy number gain See cases [RCV000449375] Chr9:62525..141006407 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020389)x3 copy number gain not specified [RCV003986800] Chr9:203861..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q33.3-34.3(chr9:128652785-141044751)x3 copy number gain See cases [RCV000447080] Chr9:128652785..141044751 [GRCh37]
Chr9:9q33.3-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138222049-141018925)x1 copy number loss See cases [RCV000446074] Chr9:138222049..141018925 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139282807-141020389)x1 copy number loss See cases [RCV000448743] Chr9:139282807..141020389 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:203864-141020389)x3 copy number gain See cases [RCV000448978] Chr9:203864..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q33.2-34.3(chr9:124642754-141146461)x3 copy number gain See cases [RCV000448784] Chr9:124642754..141146461 [GRCh37]
Chr9:9q33.2-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138209358-141020389)x1 copy number loss See cases [RCV000510584] Chr9:138209358..141020389 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138275621-141020389)x3 copy number gain See cases [RCV000511188] Chr9:138275621..141020389 [GRCh37]
Chr9:9q34.3		 likely pathogenic
NM_004669.3(CLIC3):c.691C>T (p.Pro231Ser) single nucleotide variant Inborn genetic diseases [RCV003261029] Chr9:136994701 [GRCh38]
Chr9:139889153 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q21.11-34.3(chr9:71069743-140999928) copy number gain Global developmental delay [RCV000626548] Chr9:71069743..140999928 [GRCh37]
Chr9:9q21.11-34.3		 likely pathogenic
GRCh37/hg19 9q34.13-34.3(chr9:135377559-141213431)x1 copy number loss mTOR Inhibitor response [RCV000626442] Chr9:135377559..141213431 [GRCh37]
Chr9:9q34.13-34.3		 drug response
GRCh37/hg19 9p24.3-q34.3(chr9:203862-141020389) copy number gain See cases [RCV000512392] Chr9:203862..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.13-34.3(chr9:135105971-141020389)x3 copy number gain not provided [RCV000683160] Chr9:135105971..141020389 [GRCh37]
Chr9:9q34.13-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139835558-139983339)x3 copy number gain not provided [RCV000753228] Chr9:139835558..139983339 [GRCh37]
Chr9:9q34.3		 benign
GRCh37/hg19 9q34.3(chr9:139754427-140088630)x3 copy number gain not provided [RCV000753226] Chr9:139754427..140088630 [GRCh37]
Chr9:9q34.3		 benign
GRCh37/hg19 9q34.3(chr9:139754431-140088630)x3 copy number gain not provided [RCV000753227] Chr9:139754431..140088630 [GRCh37]
Chr9:9q34.3		 benign
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141122247)x3 copy number gain not provided [RCV000748055] Chr9:10590..141122247 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:137816459-141114095)x1 copy number loss not provided [RCV000748787] Chr9:137816459..141114095 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141107672)x3 copy number gain not provided [RCV000748053] Chr9:10590..141107672 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:46587-141066491)x3 copy number gain not provided [RCV000748063] Chr9:46587..141066491 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:10590-141114095)x2 copy number gain not provided [RCV000748054] Chr9:10590..141114095 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
NM_004669.3(CLIC3):c.271T>A (p.Phe91Ile) single nucleotide variant Inborn genetic diseases [RCV003267880] Chr9:136995291 [GRCh38]
Chr9:139889743 [GRCh37]
Chr9:9q34.3		 uncertain significance
NC_000009.11:g.(?_138594085)_(140062314_?)dup duplication Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant [RCV001033771] Chr9:138594085..140062314 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9p24.3-q34.3(chr9:203861-141020388)x3 copy number gain not provided [RCV000845900] Chr9:203861..141020388 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139766260-140186072)x3 copy number gain not provided [RCV000848688] Chr9:139766260..140186072 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q21.11-34.3(chr9:71416475-141020389)x3 copy number gain not provided [RCV000847808] Chr9:71416475..141020389 [GRCh37]
Chr9:9q21.11-34.3		 pathogenic
NC_000009.11:g.(?_139089171)_(141016451_?)del deletion Rafiq syndrome [RCV003122293]|not provided [RCV003105304] Chr9:139089171..141016451 [GRCh37]
Chr9:9q34.3		 pathogenic|no classifications from unflagged records
NC_000009.11:g.(?_138645763)_(140729425_?)del deletion Developmental and epileptic encephalopathy, 14 [RCV001362982]|Kleefstra syndrome 1 [RCV001031921] Chr9:138645763..140729425 [GRCh37]
Chr9:9q34.3		 pathogenic|uncertain significance
GRCh37/hg19 9q34.3(chr9:138225001-141015001) copy number loss Microcephaly [RCV001252947] Chr9:138225001..141015001 [GRCh37]
Chr9:9q34.3		 pathogenic
NC_000009.11:g.(?_139018777)_(141018984_?)del deletion Kleefstra syndrome 1 [RCV001267844] Chr9:139018777..141018984 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139776707-140234193)x3 copy number gain not provided [RCV001259536] Chr9:139776707..140234193 [GRCh37]
Chr9:9q34.3		 uncertain significance
Single allele deletion Epilepsy [RCV001293379] Chr9:139764148..141066491 [GRCh37]
Chr9:9q34.3		 pathogenic
NC_000009.11:g.(?_139258557)_(140003427_?)del deletion Predisposition to invasive fungal disease due to CARD9 deficiency [RCV001380370] Chr9:139258557..140003427 [GRCh37]
Chr9:9q34.3		 pathogenic
NC_000009.11:g.(?_138594085)_(140062314_?)dup duplication Developmental and epileptic encephalopathy, 14 [RCV001305481]|Intellectual disability, autosomal dominant 8 [RCV001033771] Chr9:138594085..140062314 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q34.3(chr9:139284464-141018984) copy number loss Cryptorchidism [RCV001352666] Chr9:139284464..141018984 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:138740078-141020389) copy number loss not specified [RCV002052850] Chr9:138740078..141020389 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139282807-141020389) copy number loss not specified [RCV002052852] Chr9:139282807..141020389 [GRCh37]
Chr9:9q34.3		 pathogenic
GRCh37/hg19 9p24.3-q34.3(chr9:353349-141020389) copy number gain not specified [RCV002053823] Chr9:353349..141020389 [GRCh37]
Chr9:9p24.3-q34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139563039-140310033) copy number loss not specified [RCV002052853] Chr9:139563039..140310033 [GRCh37]
Chr9:9q34.3		 uncertain significance
NC_000009.11:g.(?_135139626)_(140034216_?)dup duplication Developmental and epileptic encephalopathy, 14 [RCV003111109]|Leigh syndrome [RCV003122287]|Rafiq syndrome [RCV003122286]|Tuberous sclerosis 1 [RCV003111108] Chr9:135139626..140034216 [GRCh37]
Chr9:9q34.13-34.3		 uncertain significance
NC_000009.11:g.(?_138392557)_(141016451_?)del deletion Adams-Oliver syndrome 5 [RCV003119767]|Developmental and epileptic encephalopathy, 14 [RCV003109684]|Familial aplasia of the vermis [RCV003119768] Chr9:138392557..141016451 [GRCh37]
Chr9:9q34.3		 pathogenic|uncertain significance
NC_000009.11:g.(?_131087402)_(141016451_?)dup duplication Neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome [RCV003119700] Chr9:131087402..141016451 [GRCh37]
Chr9:9q34.11-34.3		 uncertain significance
NC_000009.11:g.(?_136218768)_(141016451_?)dup duplication Kleefstra syndrome 1 [RCV003122719] Chr9:136218768..141016451 [GRCh37]
Chr9:9q34.2-34.3		 uncertain significance
NM_004669.3(CLIC3):c.592G>A (p.Glu198Lys) single nucleotide variant Inborn genetic diseases [RCV003281353] Chr9:136994800 [GRCh38]
Chr9:139889252 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.55G>A (p.Val19Met) single nucleotide variant Inborn genetic diseases [RCV002753640] Chr9:136995736 [GRCh38]
Chr9:139890188 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.346A>C (p.Ile116Leu) single nucleotide variant Inborn genetic diseases [RCV002860611] Chr9:136995216 [GRCh38]
Chr9:139889668 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.562G>A (p.Ala188Thr) single nucleotide variant Inborn genetic diseases [RCV002907403] Chr9:136994830 [GRCh38]
Chr9:139889282 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.538C>A (p.Leu180Met) single nucleotide variant Inborn genetic diseases [RCV002974583] Chr9:136994944 [GRCh38]
Chr9:139889396 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.697G>A (p.Val233Met) single nucleotide variant Inborn genetic diseases [RCV002739784] Chr9:136994695 [GRCh38]
Chr9:139889147 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.105G>T (p.Lys35Asn) single nucleotide variant Inborn genetic diseases [RCV002887287] Chr9:136995686 [GRCh38]
Chr9:139890138 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh38/hg38 9q34.3(chr9:134962336-137240181)x1 copy number loss See cases [RCV002640756] Chr9:134962336..137240181 [GRCh38]
Chr9:9q34.3		 pathogenic
NM_004669.3(CLIC3):c.557T>C (p.Val186Ala) single nucleotide variant Inborn genetic diseases [RCV002930336] Chr9:136994835 [GRCh38]
Chr9:139889287 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.533C>T (p.Pro178Leu) single nucleotide variant Inborn genetic diseases [RCV002935511] Chr9:136994949 [GRCh38]
Chr9:139889401 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.649T>C (p.Tyr217His) single nucleotide variant Inborn genetic diseases [RCV002934472] Chr9:136994743 [GRCh38]
Chr9:139889195 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.263C>T (p.Pro88Leu) single nucleotide variant Inborn genetic diseases [RCV002921455] Chr9:136995448 [GRCh38]
Chr9:139889900 [GRCh37]
Chr9:9q34.3		 uncertain significance
NM_004669.3(CLIC3):c.110T>C (p.Val37Ala) single nucleotide variant Inborn genetic diseases [RCV003360149] Chr9:136995681 [GRCh38]
Chr9:139890133 [GRCh37]
Chr9:9q34.3		 uncertain significance
GRCh37/hg19 9q34.2-34.3(chr9:136988996-141020389)x3 copy number gain not provided [RCV003484786] Chr9:136988996..141020389 [GRCh37]
Chr9:9q34.2-34.3		 pathogenic
GRCh37/hg19 9q34.3(chr9:139685408-141050580)x3 copy number gain 9q34.3 microduplication-related neurodevelopmental disorder [RCV003761660] Chr9:139685408..141050580 [GRCh37]
Chr9:9q34.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1068
Count of miRNA genes:482
Interacting mature miRNAs:555
Transcripts:ENST00000473911, ENST00000480181, ENST00000494426
Prediction methods: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.

Markers in Region
RH47857  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh379139,889,092 - 139,889,219UniSTSGRCh37
Build 369139,008,913 - 139,009,040RGDNCBI36
Celera9110,401,402 - 110,401,529RGD
Cytogenetic Map9q34.3UniSTS
HuRef9109,348,198 - 109,348,325UniSTS
GeneMap99-GB4 RH Map9420.91UniSTS


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 entire extraembryonic component
High 1 1 1 1 1 1
Medium 158 773 748 64 613 23 1887 68 572 40 345 1414 53 241 1252 3
Low 2126 2153 763 417 774 300 1506 1375 2480 291 1021 141 118 913 848
Below cutoff 137 55 208 138 140 138 848 713 637 75 76 40 1 50 668 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000473911
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,994,734 - 136,996,537 (-)Ensembl
RefSeq Acc Id: ENST00000480181
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,994,635 - 136,995,747 (-)Ensembl
RefSeq Acc Id: ENST00000494426   ⟹   ENSP00000419378
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl9136,994,608 - 136,996,568 (-)Ensembl
RefSeq Acc Id: NM_004669   ⟹   NP_004660
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh389136,994,608 - 136,996,568 (-)NCBI
GRCh379139,889,060 - 139,892,200 (-)NCBI
Build 369139,008,881 - 139,010,845 (-)NCBI Archive
Celera9110,401,370 - 110,403,334 (-)RGD
HuRef9109,348,166 - 109,350,130 (-)RGD
CHM1_19140,037,817 - 140,039,781 (-)NCBI
T2T-CHM13v2.09149,229,019 - 149,230,979 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_004660 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD16450 (Get FASTA)   NCBI Sequence Viewer  
  AAH07012 (Get FASTA)   NCBI Sequence Viewer  
  CAG46863 (Get FASTA)   NCBI Sequence Viewer  
  EAW88329 (Get FASTA)   NCBI Sequence Viewer  
  EAW88330 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000419378
  ENSP00000419378.1
GenBank Protein O95833 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_004660   ⟸   NM_004669
- UniProtKB: Q5SPZ7 (UniProtKB/Swiss-Prot),   O95833 (UniProtKB/Swiss-Prot),   Q6FGP1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000419378   ⟸   ENST00000494426
Protein Domains
GST C-terminal   GST N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O95833-F1-model_v2 AlphaFold O95833 1-236 view protein structure

Promoters
RGD ID:7216739
Promoter ID:EPDNEW_H14115
Type:multiple initiation site
Name:CLIC3_1
Description:chloride intracellular channel 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H14117  EPDNEW_H14116  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh389136,996,566 - 136,996,626EPDNEW
RGD ID:7216743
Promoter ID:EPDNEW_H14116
Type:initiation region
Name:CLIC3_3
Description:chloride intracellular channel 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H14115  EPDNEW_H14117  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh389136,996,817 - 136,996,877EPDNEW
RGD ID:7216741
Promoter ID:EPDNEW_H14117
Type:initiation region
Name:CLIC3_2
Description:chloride intracellular channel 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H14115  EPDNEW_H14116  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh389136,997,902 - 136,997,962EPDNEW
RGD ID:6807396
Promoter ID:HG_KWN:65675
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000055177
Position:
Human AssemblyChrPosition (strand)Source
Build 369139,009,831 - 139,010,537 (-)MPROMDB
RGD ID:6807397
Promoter ID:HG_KWN:65676
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000055174,   OTTHUMT00000055175,   OTTHUMT00000055176
Position:
Human AssemblyChrPosition (strand)Source
Build 369139,010,656 - 139,011,957 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2064 AgrOrtholog
COSMIC CLIC3 COSMIC
Ensembl Genes ENSG00000169583 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000494426 ENTREZGENE
  ENST00000494426.2 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1050.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutaredoxin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000169583 GTEx
HGNC ID HGNC:2064 ENTREZGENE
Human Proteome Map CLIC3 Human Proteome Map
InterPro CLIC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione-S-Trfase_C-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione-S-Trfase_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glutathione_S-Trfase UniProtKB/Swiss-Prot
  Glutathione_S-Trfase_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:9022 UniProtKB/Swiss-Prot
NCBI Gene 9022 ENTREZGENE
OMIM 606533 OMIM
PANTHER CHLORIDE INTRACELLULAR CHANNEL PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CHLORIDE INTRACELLULAR CHANNEL PROTEIN 6-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam GST_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GST_N_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA26590 PharmGKB
PRINTS INTCLCHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GST_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GST_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47616 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52833 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt CLIC3_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q5SPZ7 ENTREZGENE
  Q6FGP1 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary Q5SPZ7 UniProtKB/Swiss-Prot