CLCA1 (chloride channel accessory 1) - Rat Genome Database

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Gene: CLCA1 (chloride channel accessory 1) Homo sapiens
Analyze
Symbol: CLCA1
Name: chloride channel accessory 1
RGD ID: 1314775
HGNC Page HGNC
Description: Predicted to have intracellular calcium activated chloride channel activity. Predicted to be involved in ion transmembrane transport. Predicted to localize to integral component of plasma membrane and secretory granule. Implicated in asthma and chronic obstructive pulmonary disease. Biomarker of chronic obstructive pulmonary disease and cystic fibrosis.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: CACC; CaCC-1; CACC1; calcium-activated chloride channel family member 1; calcium-activated chloride channel protein 1; calcium-activated chloride channel regulator 1; calcium-dependent chloride channel-1; chloride channel regulator 1; chloride channel, calcium activated, family member 1; CLCA family member 1, chloride channel regulator; CLCRG1; FLJ95147; GOB5; hCaCC-1; hCLCA1
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
GRCh38.p13 Ensembl186,468,368 - 86,500,259 (+)EnsemblGRCh38hg38GRCh38
GRCh38186,468,927 - 86,500,259 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37186,934,610 - 86,965,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,707,114 - 86,738,565 (+)NCBINCBI36hg18NCBI36
Build 34186,646,071 - 86,677,963NCBI
Celera185,178,525 - 85,209,980 (+)NCBI
Cytogenetic Map1p22.3NCBI
HuRef185,045,156 - 85,076,624 (+)NCBIHuRef
CHM1_1187,049,378 - 87,080,831 (+)NCBICHM1_1
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

Additional References at PubMed
PMID:9828122   PMID:10437792   PMID:10617765   PMID:10737800   PMID:10758170   PMID:11071307   PMID:11842292   PMID:11994272   PMID:12110680   PMID:12408984   PMID:12568493   PMID:14512419  
PMID:14702039   PMID:15490240   PMID:15919655   PMID:16023076   PMID:16148052   PMID:16344560   PMID:16465045   PMID:16470849   PMID:17110338   PMID:17426222   PMID:17621552   PMID:17698377  
PMID:19307298   PMID:19423540   PMID:19530997   PMID:19834535   PMID:19913121   PMID:20179644   PMID:20406964   PMID:20438785   PMID:20464982   PMID:20542744   PMID:20628086   PMID:21762802  
PMID:21873635   PMID:22731784   PMID:23112050   PMID:23593331   PMID:24349445   PMID:25603912   PMID:25781344   PMID:26004777   PMID:28420732   PMID:28974231   PMID:29885864   PMID:31570526  
PMID:31995732  


Genomics

Comparative Map Data
CLCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl186,468,368 - 86,500,259 (+)EnsemblGRCh38hg38GRCh38
GRCh38186,468,927 - 86,500,259 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37186,934,610 - 86,965,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,707,114 - 86,738,565 (+)NCBINCBI36hg18NCBI36
Build 34186,646,071 - 86,677,963NCBI
Celera185,178,525 - 85,209,980 (+)NCBI
Cytogenetic Map1p22.3NCBI
HuRef185,045,156 - 85,076,624 (+)NCBIHuRef
CHM1_1187,049,378 - 87,080,831 (+)NCBICHM1_1
Clca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,710,298 - 144,738,537 (-)NCBIGRCm39mm39
GRCm39 Ensembl3144,709,578 - 144,738,537 (-)Ensembl
GRCm383145,004,537 - 145,032,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,003,817 - 145,032,776 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,667,501 - 144,695,740 (-)NCBIGRCm37mm9NCBIm37
MGSCv363144,941,924 - 144,970,145 (-)NCBImm8
Celera3151,445,713 - 151,476,303 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.26NCBI
Clca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22233,938,677 - 233,964,369 (-)NCBI
Rnor_6.0 Ensembl2250,897,969 - 250,923,744 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02250,897,980 - 250,923,711 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02269,425,672 - 269,451,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,057,135 - 243,084,146 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12243,043,871 - 243,070,886 (-)NCBI
Celera2225,927,785 - 225,953,924 (-)NCBICelera
Cytogenetic Map2q44NCBI
Clca1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554237,684,709 - 7,714,449 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554237,684,741 - 7,714,438 (-)NCBIChiLan1.0ChiLan1.0
CLCA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1187,852,383 - 87,884,267 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,852,599 - 87,884,751 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01118,999,099 - 119,030,839 (+)NCBIMhudiblu_PPA_v0panPan3
CLCA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1661,620,755 - 61,650,111 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl661,620,995 - 61,650,083 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha664,334,464 - 64,364,165 (-)NCBI
ROS_Cfam_1.0662,160,281 - 62,189,982 (-)NCBI
UMICH_Zoey_3.1661,693,037 - 61,722,731 (-)NCBI
UNSW_CanFamBas_1.0661,656,245 - 61,686,130 (-)NCBI
UU_Cfam_GSD_1.0662,162,204 - 62,191,927 (-)NCBI
Clca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505896,941,723 - 96,975,427 (+)NCBI
SpeTri2.0NW_004936865155,284 - 188,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,475,947 - 129,655,385 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14129,621,259 - 129,655,385 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24142,139,255 - 142,173,314 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12046,930,713 - 46,964,301 (-)NCBI
ChlSab1.1 Ensembl2046,927,412 - 46,963,737 (-)Ensembl
Vero_WHO_p1.0NW_02366603370,846,708 - 70,880,438 (+)NCBI
Clca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474211,145,406 - 11,172,369 (-)NCBI

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:57
Interacting mature miRNAs:58
Transcripts:ENST00000234701, ENST00000394711
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.


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 40 23 1
Medium 530 2 1 140 1 3 6 3 3 1 1 2
Low 267 13 16 4 34 2 43 23 19 2 300 20 3 13 26
Below cutoff 1082 1643 1086 308 597 159 2047 1274 2146 75 733 869 149 637 1332 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000234701   ⟹   ENSP00000234701
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl186,468,368 - 86,500,259 (+)Ensembl
RefSeq Acc Id: ENST00000394711   ⟹   ENSP00000378200
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl186,468,927 - 86,500,259 (+)Ensembl
RefSeq Acc Id: NM_001285   ⟹   NP_001276
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38186,468,927 - 86,500,259 (+)NCBI
GRCh37186,934,526 - 86,965,977 (+)ENTREZGENE
Build 36186,707,114 - 86,738,565 (+)NCBI Archive
HuRef185,045,156 - 85,076,624 (+)ENTREZGENE
CHM1_1187,049,378 - 87,080,831 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001276   ⟸   NM_001285
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: ENSP00000234701   ⟸   ENST00000234701
RefSeq Acc Id: ENSP00000378200   ⟸   ENST00000394711
Protein Domains
VWFA

Promoters
RGD ID:6856084
Promoter ID:EPDNEW_H1207
Type:multiple initiation site
Name:CLCA1_1
Description:chloride channel accessory 1
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
GRCh38186,468,927 - 86,468,987EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p31.1-13.3(chr1:72661709-107456880)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|See cases [RCV000051825] Chr1:72661709..107456880 [GRCh38]
Chr1:73127392..107999502 [GRCh37]
Chr1:72899980..107801025 [NCBI36]
Chr1:1p31.1-13.3
pathogenic
NM_001285.3(CLCA1):c.1126C>T (p.Pro376Ser) single nucleotide variant Malignant melanoma [RCV000064923] Chr1:86486697 [GRCh38]
Chr1:86952380 [GRCh37]
Chr1:86724968 [NCBI36]
Chr1:1p22.3
not provided
NM_001285.3(CLCA1):c.1760C>T (p.Thr587Ile) single nucleotide variant Malignant melanoma [RCV000064924] Chr1:86494266 [GRCh38]
Chr1:86959949 [GRCh37]
Chr1:86732537 [NCBI36]
Chr1:1p22.3
not provided
NM_001285.3(CLCA1):c.558-1193T>C single nucleotide variant Lung cancer [RCV000091027] Chr1:86481012 [GRCh38]
Chr1:86946695 [GRCh37]
Chr1:1p22.3
uncertain significance
GRCh38/hg38 1p31.1-21.1(chr1:83457325-104273917)x3 copy number gain See cases [RCV000135654] Chr1:83457325..104273917 [GRCh38]
Chr1:83923008..104816539 [GRCh37]
Chr1:83695596..104618062 [NCBI36]
Chr1:1p31.1-21.1
pathogenic
GRCh38/hg38 1p22.3-22.2(chr1:86228890-88466303)x1 copy number loss See cases [RCV000138370] Chr1:86228890..88466303 [GRCh38]
Chr1:86694573..88931986 [GRCh37]
Chr1:86467161..88704574 [NCBI36]
Chr1:1p22.3-22.2
uncertain significance
GRCh38/hg38 1p31.1-22.2(chr1:76419302-88628464)x1 copy number loss See cases [RCV000138957] Chr1:76419302..88628464 [GRCh38]
Chr1:76884987..89094147 [GRCh37]
Chr1:76657575..88866735 [NCBI36]
Chr1:1p31.1-22.2
pathogenic
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12
likely benign
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p31.1-22.1(chr1:72044544-92505091)x1 copy number loss See cases [RCV000510161] Chr1:72044544..92505091 [GRCh37]
Chr1:1p31.1-22.1
pathogenic
GRCh37/hg19 1p31.3-22.3(chr1:64321264-88153669)x1 copy number loss See cases [RCV000511392] Chr1:64321264..88153669 [GRCh37]
Chr1:1p31.3-22.3
pathogenic|uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44
pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44
pathogenic
NM_001285.4(CLCA1):c.1825G>A (p.Val609Ile) single nucleotide variant not provided [RCV000965555] Chr1:86494331 [GRCh38]
Chr1:86960014 [GRCh37]
Chr1:1p22.3
benign
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1
uncertain significance
Single allele deletion not provided [RCV000844927] Chr1:66085524..88429789 [GRCh37]
Chr1:1p31.3-22.2
not provided
NM_001285.4(CLCA1):c.1981T>C (p.Tyr661His) single nucleotide variant not provided [RCV000880975] Chr1:86495543 [GRCh38]
Chr1:86961226 [GRCh37]
Chr1:1p22.3
benign
NM_001285.4(CLCA1):c.2113+8A>G single nucleotide variant not provided [RCV000958842] Chr1:86495683 [GRCh38]
Chr1:86961366 [GRCh37]
Chr1:1p22.3
benign
NM_001285.4(CLCA1):c.1910C>T (p.Thr637Ile) single nucleotide variant not provided [RCV000907811] Chr1:86494416 [GRCh38]
Chr1:86960099 [GRCh37]
Chr1:1p22.3
benign
GRCh37/hg19 1p31.1-22.2(chr1:80804502-89490384)x3 copy number gain not provided [RCV001259073] Chr1:80804502..89490384 [GRCh37]
Chr1:1p31.1-22.2
likely pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2015 AgrOrtholog
COSMIC CLCA1 COSMIC
Ensembl Genes ENSG00000016490 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000234701 UniProtKB/Swiss-Prot
  ENSP00000378200 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000234701 UniProtKB/Swiss-Prot
  ENST00000394711 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.40.50.410 UniProtKB/Swiss-Prot
GTEx ENSG00000016490 GTEx
HGNC ID HGNC:2015 ENTREZGENE
Human Proteome Map CLCA1 Human Proteome Map
InterPro CLCA_chordata UniProtKB/Swiss-Prot
  CLCA_N UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  VWF_A UniProtKB/Swiss-Prot
  vWFA_dom_sf UniProtKB/Swiss-Prot
KEGG Report hsa:1179 UniProtKB/Swiss-Prot
NCBI Gene 1179 ENTREZGENE
OMIM 603906 OMIM
Pfam CLCA UniProtKB/Swiss-Prot
  VWA_2 UniProtKB/Swiss-Prot
PharmGKB PA26542 PharmGKB
PROSITE VWFA UniProtKB/Swiss-Prot
SMART VWA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot
TIGRFAMs hCaCC UniProtKB/Swiss-Prot
UniProt A8K7I4 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B2RAV5 UniProtKB/Swiss-Prot
  O95151 UniProtKB/Swiss-Prot
  Q5TDF4 UniProtKB/Swiss-Prot
  Q9UNF6 UniProtKB/Swiss-Prot
  Q9UPC6 UniProtKB/Swiss-Prot