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:2015
Description: Predicted to enable intracellularly calcium-gated chloride channel activity. Predicted to be involved in monoatomic ion transmembrane transport. Predicted to be located in extracellular region; microvillus; and zymogen granule membrane. Predicted to be active in plasma membrane. Implicated in asthma and chronic obstructive pulmonary disease. Biomarker of chronic obstructive pulmonary disease and cystic fibrosis.
Type: protein-coding
RefSeq Status: REVIEWED
Previously 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 Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,468,927 - 86,500,259 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,468,368 - 86,500,259 (+)EnsemblGRCh38hg38GRCh38
GRCh37186,934,610 - 86,965,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,707,114 - 86,738,565 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,646,071 - 86,677,963NCBI
Celera185,178,525 - 85,209,980 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,045,156 - 85,076,624 (+)NCBIHuRef
CHM1_1187,049,378 - 87,080,831 (+)NCBICHM1_1
T2T-CHM13v2.0186,308,943 - 86,340,288 (+)NCBIT2T-CHM13v2.0
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
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4,6-trinitrobenzenesulfonic acid  (ISO)
2-butoxyethanol  (ISO)
6-propyl-2-thiouracil  (ISO)
7,12-dimethyltetraphene  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
apigenin  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzo[ghi]perylene  (ISO)
beta-damascenone  (ISO)
bisphenol A  (ISO)
buta-1,3-diene  (ISO)
calcium silicate  (ISO)
carbon monoxide  (ISO)
carbon nanotube  (ISO)
carnosic acid  (ISO)
ceric oxide  (EXP,ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (ISO)
Erionite  (ISO)
ferroheme b  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (ISO)
genistein  (ISO)
heme b  (ISO)
histamine  (EXP)
hydrogen peroxide  (ISO)
isoprenaline  (ISO)
maneb  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
naphthalene  (ISO)
ozone  (ISO)
paraquat  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium dichromate  (ISO)
progesterone  (ISO)
resveratrol  (EXP,ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
sulfur dioxide  (ISO)
tamoxifen  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
trimellitic anhydride  (ISO)
vancomycin  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. Expression of HCLCA1 in cystic fibrosis lungs is associated with mucus overproduction. Hauber HP, etal., Eur Respir J. 2004 Jun;23(6):846-50.
3. CLCA1 gene polymorphisms in chronic obstructive pulmonary disease. Hegab AE, etal., J Med Genet 2004 Mar;41(3):e27.
4. Association of the hCLCA1 gene with childhood and adult asthma. Kamada F, etal., Genes Immun. 2004 Nov;5(7):540-7.
5. Role of gob-5 in mucus overproduction and airway hyperresponsiveness in asthma. Nakanishi A, etal., Proc Natl Acad Sci U S A. 2001 Apr 24;98(9):5175-80. Epub 2001 Apr 10.
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Increased expression of human calcium-activated chloride channel 1 is correlated with mucus overproduction in the airways of Chinese patients with chronic obstructive pulmonary disease. Wang K, etal., Chin Med J (Engl). 2007 Jun 20;120(12):1051-7.
9. Genome-wide profiling identifies epithelial cell genes associated with asthma and with treatment response to corticosteroids. Woodruff PG, etal., Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15858-63. Epub 2007 Sep 26.
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   PMID:36724073   PMID:37071682   PMID:38593125   PMID:38597420  


Genomics

Comparative Map Data
CLCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,468,927 - 86,500,259 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,468,368 - 86,500,259 (+)EnsemblGRCh38hg38GRCh38
GRCh37186,934,610 - 86,965,942 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,707,114 - 86,738,565 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,646,071 - 86,677,963NCBI
Celera185,178,525 - 85,209,980 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,045,156 - 85,076,624 (+)NCBIHuRef
CHM1_1187,049,378 - 87,080,831 (+)NCBICHM1_1
T2T-CHM13v2.0186,308,943 - 86,340,288 (+)NCBIT2T-CHM13v2.0
Clca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,710,298 - 144,738,537 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,709,578 - 144,738,537 (-)EnsemblGRCm39 Ensembl
GRCm383145,004,537 - 145,032,776 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,003,817 - 145,032,776 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,667,501 - 144,695,740 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,941,924 - 144,970,145 (-)NCBIMGSCv36mm8
Celera3151,445,713 - 151,476,303 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.26NCBI
Clca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82236,599,022 - 236,624,714 (-)NCBIGRCr8
mRatBN7.22233,938,677 - 233,964,369 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,938,677 - 233,964,369 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2241,727,691 - 241,753,301 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02239,617,800 - 239,643,385 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02234,485,318 - 234,510,926 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02250,897,980 - 250,923,711 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,897,969 - 250,923,744 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,425,672 - 269,451,524 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,057,135 - 243,084,146 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v21140,459,454 - 140,491,142 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11139,614,852 - 139,646,540 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01118,999,099 - 119,030,839 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1187,852,383 - 87,884,267 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,852,599 - 87,884,751 (+)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0662,160,281 - 62,189,982 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl662,160,878 - 62,189,975 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1661,693,037 - 61,722,731 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0661,656,245 - 61,686,130 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0662,162,204 - 62,191,927 (-)NCBIUU_Cfam_GSD_1.0
Clca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505896,941,723 - 96,975,427 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936865155,284 - 188,988 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLCA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,620,874 - 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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2046,927,412 - 46,963,737 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603370,846,708 - 70,880,438 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Clca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474211,145,413 - 11,172,369 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474211,145,406 - 11,172,369 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CLCA1
51 total Variants

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
NM_001285.4(CLCA1):c.1735G>A (p.Val579Ile) single nucleotide variant not specified [RCV004320584] Chr1:86494241 [GRCh38]
Chr1:86959924 [GRCh37]
Chr1:1p22.3		 uncertain significance
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
NM_001285.4(CLCA1):c.1322C>T (p.Ala441Val) single nucleotide variant not specified [RCV004320490] Chr1:86489135 [GRCh38]
Chr1:86954818 [GRCh37]
Chr1:1p22.3		 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
NM_001285.4(CLCA1):c.2046C>G (p.Asn682Lys) single nucleotide variant not provided [RCV001688616] Chr1:86495608 [GRCh38]
Chr1:86961291 [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
GRCh37/hg19 1p31.3-22.1(chr1:68180293-92731957) copy number loss not specified [RCV002053392] Chr1:68180293..92731957 [GRCh37]
Chr1:1p31.3-22.1		 pathogenic
NM_001285.4(CLCA1):c.2639C>T (p.Thr880Met) single nucleotide variant not specified [RCV004305264] Chr1:86499939 [GRCh38]
Chr1:86965622 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.85A>C (p.Asn29His) single nucleotide variant not specified [RCV004325029] Chr1:86469056 [GRCh38]
Chr1:86934739 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1360G>C (p.Gly454Arg) single nucleotide variant not specified [RCV004128649] Chr1:86491267 [GRCh38]
Chr1:86956950 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.726T>A (p.His242Gln) single nucleotide variant not specified [RCV004144115] Chr1:86482373 [GRCh38]
Chr1:86948056 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2057G>A (p.Arg686Gln) single nucleotide variant not specified [RCV004206633] Chr1:86495619 [GRCh38]
Chr1:86961302 [GRCh37]
Chr1:1p22.3		 likely benign
NM_001285.4(CLCA1):c.1685G>A (p.Gly562Asp) single nucleotide variant not specified [RCV004211769] Chr1:86494191 [GRCh38]
Chr1:86959874 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.432A>T (p.Leu144Phe) single nucleotide variant not specified [RCV004202691] Chr1:86473857 [GRCh38]
Chr1:86939540 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2068C>A (p.Pro690Thr) single nucleotide variant not specified [RCV004203557] Chr1:86495630 [GRCh38]
Chr1:86961313 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.109G>A (p.Val37Ile) single nucleotide variant not specified [RCV004241449] Chr1:86469080 [GRCh38]
Chr1:86934763 [GRCh37]
Chr1:1p22.3		 likely benign
NM_001285.4(CLCA1):c.1043C>T (p.Thr348Ile) single nucleotide variant not specified [RCV004130972] Chr1:86486614 [GRCh38]
Chr1:86952297 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1213T>C (p.Ser405Pro) single nucleotide variant not specified [RCV004187520] Chr1:86489026 [GRCh38]
Chr1:86954709 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.388G>A (p.Glu130Lys) single nucleotide variant not specified [RCV004175440] Chr1:86473813 [GRCh38]
Chr1:86939496 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.15G>T (p.Lys5Asn) single nucleotide variant not specified [RCV004080159] Chr1:86468986 [GRCh38]
Chr1:86934669 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1748C>T (p.Ala583Val) single nucleotide variant not specified [RCV004195311] Chr1:86494254 [GRCh38]
Chr1:86959937 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1627G>T (p.Val543Leu) single nucleotide variant not specified [RCV004164938] Chr1:86493546 [GRCh38]
Chr1:86959229 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1819C>T (p.Pro607Ser) single nucleotide variant not specified [RCV004180483] Chr1:86494325 [GRCh38]
Chr1:86960008 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1790C>T (p.Thr597Met) single nucleotide variant not specified [RCV004216683] Chr1:86494296 [GRCh38]
Chr1:86959979 [GRCh37]
Chr1:1p22.3		 likely benign
NM_001285.4(CLCA1):c.1453C>T (p.Arg485Cys) single nucleotide variant not specified [RCV004254786] Chr1:86491360 [GRCh38]
Chr1:86957043 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.626G>T (p.Arg209Ile) single nucleotide variant not specified [RCV004297287] Chr1:86482273 [GRCh38]
Chr1:86947956 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2278A>C (p.Lys760Gln) single nucleotide variant not specified [RCV004264765] Chr1:86498736 [GRCh38]
Chr1:86964419 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1684G>A (p.Gly562Ser) single nucleotide variant not specified [RCV004349595] Chr1:86494190 [GRCh38]
Chr1:86959873 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.968T>C (p.Leu323Pro) single nucleotide variant not specified [RCV004363964] Chr1:86486539 [GRCh38]
Chr1:86952222 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.349C>T (p.Pro117Ser) single nucleotide variant not specified [RCV004357005] Chr1:86473774 [GRCh38]
Chr1:86939457 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.498T>A (p.Phe166Leu) single nucleotide variant not specified [RCV004344739] Chr1:86476494 [GRCh38]
Chr1:86942177 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2123A>G (p.Gln708Arg) single nucleotide variant not specified [RCV004358378] Chr1:86498581 [GRCh38]
Chr1:86964264 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1247A>G (p.Asn416Ser) single nucleotide variant not specified [RCV004361215] Chr1:86489060 [GRCh38]
Chr1:86954743 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1517T>A (p.Val506Glu) single nucleotide variant not specified [RCV004356003] Chr1:86493436 [GRCh38]
Chr1:86959119 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.335C>T (p.Pro112Leu) single nucleotide variant not specified [RCV004360625] Chr1:86473760 [GRCh38]
Chr1:86939443 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2423A>T (p.Gln808Leu) single nucleotide variant not specified [RCV004357475] Chr1:86499723 [GRCh38]
Chr1:86965406 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1172C>T (p.Ser391Leu) single nucleotide variant not specified [RCV004444177] Chr1:86486743 [GRCh38]
Chr1:86952426 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1676C>T (p.Ala559Val) single nucleotide variant not specified [RCV004444180] Chr1:86493595 [GRCh38]
Chr1:86959278 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1709C>T (p.Ala570Val) single nucleotide variant not specified [RCV004444181] Chr1:86494215 [GRCh38]
Chr1:86959898 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2279A>G (p.Lys760Arg) single nucleotide variant not specified [RCV004444183] Chr1:86498737 [GRCh38]
Chr1:86964420 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.620C>T (p.Thr207Ile) single nucleotide variant not specified [RCV004444187] Chr1:86482267 [GRCh38]
Chr1:86947950 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.731A>G (p.Asp244Gly) single nucleotide variant not specified [RCV004444188] Chr1:86482378 [GRCh38]
Chr1:86948061 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1873A>G (p.Ser625Gly) single nucleotide variant not specified [RCV004444182] Chr1:86494379 [GRCh38]
Chr1:86960062 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.448C>A (p.Gln150Lys) single nucleotide variant not specified [RCV004444186] Chr1:86473873 [GRCh38]
Chr1:86939556 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.15G>C (p.Lys5Asn) single nucleotide variant not specified [RCV004444179] Chr1:86468986 [GRCh38]
Chr1:86934669 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1547C>G (p.Thr516Ser) single nucleotide variant not specified [RCV004444178] Chr1:86493466 [GRCh38]
Chr1:86959149 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2582G>A (p.Arg861Gln) single nucleotide variant not specified [RCV004444184] Chr1:86499882 [GRCh38]
Chr1:86965565 [GRCh37]
Chr1:1p22.3		 likely benign
GRCh37/hg19 1p31.1-22.3(chr1:73616197-87012961)x1 copy number loss not provided [RCV003885448] Chr1:73616197..87012961 [GRCh37]
Chr1:1p31.1-22.3		 likely pathogenic
NM_001285.4(CLCA1):c.1306G>A (p.Ala436Thr) single nucleotide variant not specified [RCV004612812] Chr1:86489119 [GRCh38]
Chr1:86954802 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.2461T>A (p.Ser821Thr) single nucleotide variant not specified [RCV004612811] Chr1:86499761 [GRCh38]
Chr1:86965444 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1868G>A (p.Arg623Lys) single nucleotide variant not specified [RCV004612814] Chr1:86494374 [GRCh38]
Chr1:86960057 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1657C>T (p.Leu553Phe) single nucleotide variant not specified [RCV004612813] Chr1:86493576 [GRCh38]
Chr1:86959259 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_001285.4(CLCA1):c.1205C>A (p.Thr402Asn) single nucleotide variant not specified [RCV004612810] Chr1:86489018 [GRCh38]
Chr1:86954701 [GRCh37]
Chr1:1p22.3		 uncertain significance
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.


QTLs in Region (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407204450GWAS853426_Htriclosan measurement, 8-hydroxydeoxyguanosine measurement QTL GWAS853426 (human)3e-08triclosan measurement, 8-hydroxydeoxyguanosine measurement18647989986479900Human
2316890GLUCO302_HGlucose level QTL 302 (human)0.005Glucose level16853299294532992Human
2289499BW445_HBody weight QTL 445 (human)2.26Body morphometrywaist to hip ratio16853299294532992Human
407053401GWAS702377_Htrauma exposure measurement QTL GWAS702377 (human)0.000008trauma exposure measurement18648138586481386Human
1581539BP75_HBlood pressure QTL 75 (human)2.40.001Blood pressurepulse pressure16853299294532992Human
2292793PRSTS24_HProstate tumor susceptibility QTL 24 (human)Prostate tumor susceptibilitylate onset16853299294532992Human
1559226SLEP4_HSerum leptin concentration QTL 4 (human)3.4Hormone levelleptin181532913107532913Human


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
651 1919 1360 1351 2869 1104 1255 1 313 794 162 1127 3913 3509 16 2168 395 1273 891 152

Sequence


Ensembl Acc Id: ENST00000234701   ⟹   ENSP00000234701
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl186,468,368 - 86,500,259 (+)Ensembl
Ensembl Acc Id: ENST00000394711   ⟹   ENSP00000378200
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 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
T2T-CHM13v2.0186,308,943 - 86,340,288 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001276   ⟸   NM_001285
- Peptide Label: precursor
- UniProtKB: Q9UNF6 (UniProtKB/Swiss-Prot),   Q5TDF4 (UniProtKB/Swiss-Prot),   O95151 (UniProtKB/Swiss-Prot),   B2RAV5 (UniProtKB/Swiss-Prot),   A8K7I4 (UniProtKB/Swiss-Prot),   Q9UPC6 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSP00000234701   ⟸   ENST00000234701
Ensembl Acc Id: ENSP00000378200   ⟸   ENST00000394711
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A8K7I4-F1-model_v2 AlphaFold A8K7I4 1-914 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2015 AgrOrtholog
COSMIC CLCA1 COSMIC
Ensembl Genes ENSG00000016490 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000234701.7 UniProtKB/Swiss-Prot
  ENST00000394711 ENTREZGENE
  ENST00000394711.2 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
  CLCR 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
PANTHER CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR UniProtKB/Swiss-Prot
  CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR 1 UniProtKB/Swiss-Prot
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
UniProt A8K7I4 ENTREZGENE
  B2RAV5 ENTREZGENE
  CLCA1_HUMAN UniProtKB/Swiss-Prot
  O95151 ENTREZGENE
  Q5TDF4 ENTREZGENE
  Q9UNF6 ENTREZGENE
  Q9UPC6 ENTREZGENE
UniProt Secondary B2RAV5 UniProtKB/Swiss-Prot
  O95151 UniProtKB/Swiss-Prot
  Q5TDF4 UniProtKB/Swiss-Prot
  Q9UNF6 UniProtKB/Swiss-Prot
  Q9UPC6 UniProtKB/Swiss-Prot