CLCC1

chloride channel CLIC like 1, the group of Tetraspan junctional complex superfamily

Basic information

Region (hg38): 1:108881885-108963527

Links

ENSG00000121940

∙ NCBI:23155 ∙ OMIM:617539 ∙ HGNC:29675 ∙ Uniprot:Q96S66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 32	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	16189710; 30157172

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLCC1 gene.

Chudley-McCullough syndrome (7 variants)
not provided (6 variants)
Hearing loss, autosomal recessive (2 variants)
not specified (1 variants)
Breast-ovarian cancer, familial, susceptibility to, 2 (1 variants)
Inborn genetic diseases (1 variants)
Rare genetic deafness (1 variants)
GPSM2-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLCC1 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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			3 clinvar	70 clinvar	5 clinvar	78
missense		1 clinvar	133 clinvar	5 clinvar	6 clinvar	145
nonsense			4 clinvar			4
start loss						0
frameshift			11 clinvar			11
splice donor/acceptor (+/-2bp)			6 clinvar	1 clinvar		7
Total	0	1	157	76	11

Highest pathogenic variant AF is 0.0000591545

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLCC1	protein_coding	protein_coding	ENST00000369971	10	33982

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00620	0.994	125677	0	70	125747	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	245	298	0.821	0.0000155	3601
Missense in Polyphen		77	109.67	0.70212		1465
Synonymous	0.0567	110	111	0.993	0.00000620	1027
Loss of Function	3.29	9	27.7	0.325	0.00000133	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00125	0.00116
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000660	0.000653
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000660	0.000653
South Asian	0.000135	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to act as a chloride ion channel. {ECO:0000250}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

loftool: 0.991
rvis_EVS: 1.04
rvis_percentile_EVS: 91.31

Haploinsufficiency Scores

pHI: 0.131
hipred: N
hipred_score: 0.233
ghis: 0.479

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.147

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Clcc1
Phenotype: muscle phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: chloride transmembrane transport
Cellular component: nucleus;endoplasmic reticulum;Golgi apparatus;membrane;chloride channel complex;intracellular membrane-bounded organelle
Molecular function: chloride channel activity