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.

• not_provided (283 variants)
• not_specified (75 variants)
• Retinitis_pigmentosa_32 (3 variants)
• Retinal_dystrophy (2 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: NM_001377458.1. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	77	4	84
missense		1	150	11	3	165
nonsense			5			5
start loss						0
frameshift			11			11
splice donor/acceptor (+/-2bp)			6	1		7
Total	0	1	175	89	7

Highest pathogenic variant AF is 0.000023559141

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
		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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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

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