CLIC6

chloride intracellular channel 6, the group of Chloride intracellular channels

Basic information

Region (hg38): 21:34668994-34718227

Previous symbols: [ "CLIC1L" ]

Links

ENSG00000159212NCBI:54102OMIM:615321HGNC:2065Uniprot:Q96NY7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLIC6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLIC6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
9
clinvar
3
clinvar
12
missense
52
clinvar
4
clinvar
6
clinvar
62
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 52 13 10

Variants in CLIC6

This is a list of pathogenic ClinVar variants found in the CLIC6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
21-34669392-G-C not specified Uncertain significance (Aug 26, 2024)3493675
21-34669426-G-A not specified Uncertain significance (Aug 09, 2021)2241480
21-34669441-C-T not specified Uncertain significance (Jun 25, 2024)3493667
21-34669473-G-A not specified Uncertain significance (Jul 02, 2024)3493671
21-34669477-A-T not specified Uncertain significance (Mar 24, 2023)2564414
21-34669516-G-C not specified Likely benign (Nov 17, 2023)3145770
21-34669521-G-C not specified Uncertain significance (Nov 10, 2024)3145772
21-34669543-G-T not specified Uncertain significance (Jul 30, 2024)3493662
21-34669566-G-T not specified Uncertain significance (Aug 02, 2021)2407794
21-34669605-G-T not specified Uncertain significance (Aug 12, 2024)3493674
21-34669615-C-T not specified Uncertain significance (Dec 13, 2022)2362921
21-34669618-G-C not specified Uncertain significance (Jan 04, 2024)3145781
21-34669629-G-A not specified Uncertain significance (Jun 06, 2022)2207780
21-34669636-C-T not specified Uncertain significance (Nov 17, 2023)3145782
21-34669656-C-T not specified Uncertain significance (Jun 28, 2024)3493670
21-34669669-A-G not specified Uncertain significance (Nov 24, 2024)3493666
21-34669671-G-A not specified Uncertain significance (Dec 06, 2022)3145783
21-34669698-G-A not specified Likely benign (Feb 27, 2023)2489785
21-34669725-C-T not specified Uncertain significance (Nov 14, 2023)3145784
21-34669803-G-A not specified Uncertain significance (Oct 03, 2023)3145785
21-34669836-G-A not specified Uncertain significance (May 28, 2024)3267736
21-34669859-G-A Likely benign (Apr 01, 2024)3234167
21-34669864-G-A not specified Uncertain significance (Mar 29, 2023)2531174
21-34669898-A-G not specified Uncertain significance (Sep 16, 2021)2250496
21-34669919-C-G Likely benign (Dec 31, 2019)715385

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLIC6protein_codingprotein_codingENST00000349499 648838
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003530.8301257080391257470.000155
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6812202500.8790.00001324341
Missense in Polyphen95106.160.894891417
Synonymous-0.3441121071.040.000006601378
Loss of Function1.30914.30.6286.13e-7247

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002750.000275
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.000.00
European (Non-Finnish)0.0001850.000185
Middle Eastern0.0003260.000326
South Asian0.0002300.000229
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May insert into membranes and form chloride ion channels. May play a critical role in water-secreting cells, possibly through the regulation of chloride ion transport (By similarity). {ECO:0000250}.;

Recessive Scores

pRec
0.131

Haploinsufficiency Scores

pHI
0.0892
hipred
N
hipred_score
0.247
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.390

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Clic6
Phenotype

Zebrafish Information Network

Gene name
clic6
Affected structure
otolith
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
regulation of ion transmembrane transport;chloride transmembrane transport
Cellular component
cytoplasm;plasma membrane;chloride channel complex;extracellular exosome
Molecular function
voltage-gated ion channel activity;chloride channel activity;D2 dopamine receptor binding;D3 dopamine receptor binding;D4 dopamine receptor binding