CLCA4 (chloride channel accessory 4) - Rat Genome Database

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Gene: CLCA4 (chloride channel accessory 4) Homo sapiens
Analyze
Symbol: CLCA4
Name: chloride channel accessory 4
RGD ID: 1351138
HGNC Page HGNC:2018
Description: Predicted to enable intracellular calcium activated chloride channel activity and ligand-gated monoatomic ion channel activity. Predicted to be involved in monoatomic ion transmembrane transport. Predicted to act upstream of or within chloride transport. Predicted to be located in apical plasma membrane and extracellular region. Predicted to be active in plasma membrane.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: CaCC; caCC-2; CaCC2; calcium-activated chloride channel family member 4; calcium-activated chloride channel protein 2; calcium-activated chloride channel regulator 4; chloride channel regulator 4; chloride channel, calcium activated, family member 4; hCaCC-2; hCLCA4; MGC142247; MGC142249
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Pig
Green Monkey
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
GRCh38186,547,078 - 86,580,754 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,547,078 - 86,580,754 (+)EnsemblGRCh38hg38GRCh38
GRCh37187,012,761 - 87,046,437 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,785,347 - 86,819,025 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,724,781 - 86,758,451NCBI
Celera185,256,746 - 85,290,417 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,123,236 - 85,156,884 (+)NCBIHuRef
CHM1_1187,127,607 - 87,161,285 (+)NCBICHM1_1
T2T-CHM13v2.0186,387,119 - 86,420,795 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10437792   PMID:10758170   PMID:11071307   PMID:12477932   PMID:12975309   PMID:15490240   PMID:16344560   PMID:19460752   PMID:21873635   PMID:23073314   PMID:23376485  
PMID:24386311   PMID:24623722   PMID:28298427   PMID:30312171   PMID:30887952   PMID:31164625   PMID:32296183   PMID:32773719   PMID:32797167   PMID:33961781  


Genomics

Comparative Map Data
CLCA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,547,078 - 86,580,754 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,547,078 - 86,580,754 (+)EnsemblGRCh38hg38GRCh38
GRCh37187,012,761 - 87,046,437 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,785,347 - 86,819,025 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,724,781 - 86,758,451NCBI
Celera185,256,746 - 85,290,417 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,123,236 - 85,156,884 (+)NCBIHuRef
CHM1_1187,127,607 - 87,161,285 (+)NCBICHM1_1
T2T-CHM13v2.0186,387,119 - 86,420,795 (+)NCBIT2T-CHM13v2.0
Clca4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,658,247 - 144,680,806 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,658,241 - 144,680,806 (-)EnsemblGRCm39 Ensembl
GRCm383144,952,486 - 144,975,045 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3144,952,480 - 144,975,045 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,615,450 - 144,638,009 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,890,061 - 144,912,397 (-)NCBIMGSCv36mm8
Celera3151,393,608 - 151,416,192 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.22NCBI
Clca4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82236,543,975 - 236,565,096 (-)NCBIGRCr8
mRatBN7.22233,883,625 - 233,904,993 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2233,883,851 - 233,903,089 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.02250,842,939 - 250,864,060 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2250,843,165 - 250,862,419 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02269,371,177 - 269,392,072 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42243,002,320 - 243,023,215 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12242,989,059 - 243,009,955 (-)NCBI
Celera2225,872,978 - 225,893,873 (-)NCBICelera
Cytogenetic Map2q44NCBI
CLCA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21140,379,779 - 140,446,580 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11139,535,186 - 139,601,980 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01119,077,318 - 119,111,027 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1187,930,549 - 87,964,225 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl187,930,549 - 87,964,218 (+)Ensemblpanpan1.1panPan2
CLCA4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1661,559,472 - 61,584,601 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl661,559,738 - 61,584,177 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha664,273,532 - 64,298,313 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0662,099,324 - 62,124,119 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl662,099,597 - 62,124,493 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1661,632,408 - 61,657,193 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0661,595,579 - 61,620,375 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0662,096,317 - 62,126,025 (-)NCBIUU_Cfam_GSD_1.0
CLCA4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4129,491,594 - 129,599,410 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14129,562,573 - 129,593,123 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24142,080,452 - 142,110,275 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLCA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12046,856,330 - 46,890,832 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2046,856,232 - 46,890,515 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603370,921,065 - 70,954,895 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in CLCA4
41 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_012128.3(CLCA4):c.219C>T (p.Phe73=) single nucleotide variant Malignant melanoma [RCV000064925] Chr1:86559991 [GRCh38]
Chr1:87025674 [GRCh37]
Chr1:86798262 [NCBI36]
Chr1:1p22.3		 not provided
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
NM_012128.4(CLCA4):c.1321G>A (p.Ala441Thr) single nucleotide variant Inborn genetic diseases [RCV003304171] Chr1:86571215 [GRCh38]
Chr1:87036898 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2324C>T (p.Thr775Ile) single nucleotide variant Inborn genetic diseases [RCV003306948] Chr1:86579555 [GRCh38]
Chr1:87045238 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.743A>T (p.Glu248Val) single nucleotide variant Inborn genetic diseases [RCV003281464] Chr1:86565809 [GRCh38]
Chr1:87031492 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1058C>T (p.Ala353Val) single nucleotide variant Inborn genetic diseases [RCV003279318] Chr1:86567527 [GRCh38]
Chr1:87033210 [GRCh37]
Chr1:1p22.3		 uncertain significance
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
GRCh37/hg19 1p22.3(chr1:87015179-87085266)x3 copy number gain not provided [RCV000736558] Chr1:87015179..87085266 [GRCh37]
Chr1:1p22.3		 benign
GRCh37/hg19 1p22.3(chr1:87020617-87036922)x1 copy number loss not provided [RCV000736559] Chr1:87020617..87036922 [GRCh37]
Chr1:1p22.3		 benign
GRCh37/hg19 1p22.3(chr1:87028669-87036040)x1 copy number loss not provided [RCV000736560] Chr1:87028669..87036040 [GRCh37]
Chr1:1p22.3		 benign
GRCh37/hg19 1p22.3(chr1:87028669-87036922)x1 copy number loss not provided [RCV000736561] Chr1:87028669..87036922 [GRCh37]
Chr1:1p22.3		 benign
NM_012128.4(CLCA4):c.1474A>G (p.Ser492Gly) single nucleotide variant not provided [RCV000970418] Chr1:86574546 [GRCh38]
Chr1:87040229 [GRCh37]
Chr1:1p22.3		 benign
Single allele deletion not provided [RCV000844927] Chr1:66085524..88429789 [GRCh37]
Chr1:1p31.3-22.2		 not provided
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_012128.4(CLCA4):c.339A>G (p.Arg113=) single nucleotide variant not provided [RCV000952853] Chr1:86560249 [GRCh38]
Chr1:87025932 [GRCh37]
Chr1:1p22.3		 benign|likely benign
NM_012128.4(CLCA4):c.895T>C (p.Leu299=) single nucleotide variant not provided [RCV000913239] Chr1:86565961 [GRCh38]
Chr1:87031644 [GRCh37]
Chr1:1p22.3		 benign
NM_012128.4(CLCA4):c.405del (p.Asp136fs) deletion not provided [RCV000955732] Chr1:86560315 [GRCh38]
Chr1:87025998 [GRCh37]
Chr1:1p22.3		 likely 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
NM_012128.4(CLCA4):c.1453C>T (p.Gln485Ter) single nucleotide variant not provided [RCV001815676] Chr1:86572706 [GRCh38]
Chr1:87038389 [GRCh37]
Chr1:1p22.3		 uncertain significance
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_012128.4(CLCA4):c.2654C>A (p.Pro885His) single nucleotide variant Inborn genetic diseases [RCV002731933] Chr1:86580239 [GRCh38]
Chr1:87045922 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.346C>A (p.Pro116Thr) single nucleotide variant Inborn genetic diseases [RCV002841550] Chr1:86560256 [GRCh38]
Chr1:87025939 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2134G>A (p.Ala712Thr) single nucleotide variant Inborn genetic diseases [RCV002911414] Chr1:86579365 [GRCh38]
Chr1:87045048 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1103G>A (p.Arg368Lys) single nucleotide variant Inborn genetic diseases [RCV002759017] Chr1:86567572 [GRCh38]
Chr1:87033255 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2725G>A (p.Val909Ile) single nucleotide variant Inborn genetic diseases [RCV002888846] Chr1:86580310 [GRCh38]
Chr1:87045993 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.401C>T (p.Thr134Ile) single nucleotide variant Inborn genetic diseases [RCV002926375] Chr1:86560311 [GRCh38]
Chr1:87025994 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.482G>A (p.Arg161Gln) single nucleotide variant Inborn genetic diseases [RCV002823449] Chr1:86563694 [GRCh38]
Chr1:87029377 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1730C>T (p.Thr577Ile) single nucleotide variant Inborn genetic diseases [RCV002924016] Chr1:86575378 [GRCh38]
Chr1:87041061 [GRCh37]
Chr1:1p22.3		 likely benign
NM_012128.4(CLCA4):c.1414G>A (p.Ala472Thr) single nucleotide variant Inborn genetic diseases [RCV002660814] Chr1:86572667 [GRCh38]
Chr1:87038350 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2681G>T (p.Gly894Val) single nucleotide variant Inborn genetic diseases [RCV002823314] Chr1:86580266 [GRCh38]
Chr1:87045949 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1831A>G (p.Met611Val) single nucleotide variant Inborn genetic diseases [RCV002955647] Chr1:86575479 [GRCh38]
Chr1:87041162 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1277T>A (p.Val426Glu) single nucleotide variant Inborn genetic diseases [RCV002665221] Chr1:86571171 [GRCh38]
Chr1:87036854 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2362C>T (p.Arg788Cys) single nucleotide variant Inborn genetic diseases [RCV002956092] Chr1:86579947 [GRCh38]
Chr1:87045630 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.964C>T (p.Arg322Cys) single nucleotide variant Inborn genetic diseases [RCV002987141] Chr1:86567433 [GRCh38]
Chr1:87033116 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1234A>G (p.Thr412Ala) single nucleotide variant Inborn genetic diseases [RCV002826279] Chr1:86571128 [GRCh38]
Chr1:87036811 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2018G>A (p.Arg673Lys) single nucleotide variant Inborn genetic diseases [RCV002853655] Chr1:86577968 [GRCh38]
Chr1:87043651 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1619T>C (p.Met540Thr) single nucleotide variant Inborn genetic diseases [RCV002941856] Chr1:86574691 [GRCh38]
Chr1:87040374 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1142G>A (p.Gly381Glu) single nucleotide variant Inborn genetic diseases [RCV002960866] Chr1:86567611 [GRCh38]
Chr1:87033294 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.424A>C (p.Lys142Gln) single nucleotide variant Inborn genetic diseases [RCV002855634] Chr1:86560334 [GRCh38]
Chr1:87026017 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.931C>T (p.Leu311Phe) single nucleotide variant Inborn genetic diseases [RCV002657229] Chr1:86565997 [GRCh38]
Chr1:87031680 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.838G>A (p.Glu280Lys) single nucleotide variant Inborn genetic diseases [RCV002679428] Chr1:86565904 [GRCh38]
Chr1:87031587 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.334G>A (p.Gly112Ser) single nucleotide variant Inborn genetic diseases [RCV003256965] Chr1:86560244 [GRCh38]
Chr1:87025927 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1063A>G (p.Ile355Val) single nucleotide variant Inborn genetic diseases [RCV003257746] Chr1:86567532 [GRCh38]
Chr1:87033215 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2228A>T (p.Gln743Leu) single nucleotide variant Inborn genetic diseases [RCV003185516] Chr1:86579459 [GRCh38]
Chr1:87045142 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.2013T>G (p.Asn671Lys) single nucleotide variant Inborn genetic diseases [RCV003195572] Chr1:86577963 [GRCh38]
Chr1:87043646 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.115G>C (p.Asp39His) single nucleotide variant Inborn genetic diseases [RCV003178906] Chr1:86547234 [GRCh38]
Chr1:87012917 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1268T>C (p.Ile423Thr) single nucleotide variant Inborn genetic diseases [RCV003340251] Chr1:86571162 [GRCh38]
Chr1:87036845 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1529A>G (p.Asp510Gly) single nucleotide variant Inborn genetic diseases [RCV003350994] Chr1:86574601 [GRCh38]
Chr1:87040284 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.565G>A (p.Ala189Thr) single nucleotide variant Inborn genetic diseases [RCV003374930] Chr1:86565281 [GRCh38]
Chr1:87030964 [GRCh37]
Chr1:1p22.3		 likely benign
NM_012128.4(CLCA4):c.2236A>G (p.Ser746Gly) single nucleotide variant Inborn genetic diseases [RCV003352692] Chr1:86579467 [GRCh38]
Chr1:87045150 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.883C>T (p.Pro295Ser) single nucleotide variant Inborn genetic diseases [RCV003368671] Chr1:86565949 [GRCh38]
Chr1:87031632 [GRCh37]
Chr1:1p22.3		 uncertain significance
NM_012128.4(CLCA4):c.1251C>T (p.Asn417=) single nucleotide variant not provided [RCV003406588] Chr1:86571145 [GRCh38]
Chr1:87036828 [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
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:321
Count of miRNA genes:217
Interacting mature miRNAs:224
Transcripts:ENST00000263723, ENST00000370563, ENST00000496322
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component
High 31 1 1
Medium 374 2 3 34 79 130 30 185 24 162 11 35 5 25
Low 494 48 58 132 93 6 1182 180 2286 24 550 79 129 1 43 650 1
Below cutoff 1313 2170 1260 214 918 213 2278 1582 1038 94 526 1117 5 1069 1658 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_012128 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_024602 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011541015 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054335141 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF127035 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK000072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK000138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK293766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK307785 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK307898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK314430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL122002 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY358470 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC113687 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC113689 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB851641 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471097 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA668017 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA761219 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  HF583905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000370563   ⟹   ENSP00000359594
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl186,547,078 - 86,580,754 (+)Ensembl
RefSeq Acc Id: ENST00000496322
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl186,571,116 - 86,572,956 (+)Ensembl
RefSeq Acc Id: NM_012128   ⟹   NP_036260
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38186,547,078 - 86,580,754 (+)NCBI
GRCh37187,012,759 - 87,046,437 (+)RGD
Build 36186,785,347 - 86,819,025 (+)NCBI Archive
Celera185,256,746 - 85,290,417 (+)RGD
HuRef185,123,236 - 85,156,884 (+)ENTREZGENE
CHM1_1187,127,607 - 87,161,285 (+)NCBI
T2T-CHM13v2.0186,387,119 - 86,420,795 (+)NCBI
Sequence:
RefSeq Acc Id: NR_024602
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38186,547,078 - 86,580,754 (+)NCBI
GRCh37187,012,759 - 87,046,437 (+)RGD
Celera185,256,746 - 85,290,417 (+)RGD
HuRef185,123,236 - 85,156,884 (+)ENTREZGENE
CHM1_1187,127,607 - 87,161,285 (+)NCBI
T2T-CHM13v2.0186,387,119 - 86,420,795 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011541015   ⟹   XP_011539317
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38186,549,269 - 86,580,754 (+)NCBI
Sequence:
RefSeq Acc Id: XM_054335141   ⟹   XP_054191116
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0186,389,309 - 86,420,795 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_036260   ⟸   NM_012128
- Peptide Label: precursor
- UniProtKB: Q6UX81 (UniProtKB/Swiss-Prot),   B7Z1Q5 (UniProtKB/Swiss-Prot),   A8MQC9 (UniProtKB/Swiss-Prot),   Q9UNF7 (UniProtKB/Swiss-Prot),   Q14CN2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011539317   ⟸   XM_011541015
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000359594   ⟸   ENST00000370563
RefSeq Acc Id: XP_054191116   ⟸   XM_054335141
- Peptide Label: isoform X1
Protein Domains
VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q14CN2-F1-model_v2 AlphaFold Q14CN2 1-919 view protein structure

Promoters
RGD ID:6856086
Promoter ID:EPDNEW_H1208
Type:multiple initiation site
Name:CLCA4_1
Description:chloride channel accessory 4
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
GRCh38186,547,078 - 86,547,138EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:2018 AgrOrtholog
COSMIC CLCA4 COSMIC
Ensembl Genes ENSG00000016602 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000370563 ENTREZGENE
  ENST00000370563.3 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot
  3.40.50.410 UniProtKB/Swiss-Prot
GTEx ENSG00000016602 GTEx
HGNC ID HGNC:2018 ENTREZGENE
Human Proteome Map CLCA4 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:22802 UniProtKB/Swiss-Prot
NCBI Gene 22802 ENTREZGENE
OMIM 616857 OMIM
PANTHER CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR UniProtKB/Swiss-Prot
  CALCIUM-ACTIVATED CHLORIDE CHANNEL REGULATOR 4 UniProtKB/Swiss-Prot
Pfam CLCA UniProtKB/Swiss-Prot
  VWA UniProtKB/Swiss-Prot
PharmGKB PA26545 PharmGKB
PROSITE VWFA UniProtKB/Swiss-Prot
SMART VWA UniProtKB/Swiss-Prot
Superfamily-SCOP SSF53300 UniProtKB/Swiss-Prot
UniProt A8MQC9 ENTREZGENE
  B7Z1Q5 ENTREZGENE
  CLCA4_HUMAN UniProtKB/Swiss-Prot
  L8ECE0_HUMAN UniProtKB/TrEMBL
  Q14CN2 ENTREZGENE
  Q6UX81 ENTREZGENE
  Q9UNF7 ENTREZGENE
UniProt Secondary A8MQC9 UniProtKB/Swiss-Prot
  B7Z1Q5 UniProtKB/Swiss-Prot
  Q6UX81 UniProtKB/Swiss-Prot
  Q9UNF7 UniProtKB/Swiss-Prot