CLCC1

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

Basic information

Region (hg38): 1:108881884-108963527

Links

ENSG00000121940 ∙ NCBI:23155 ∙ OMIM:617539 ∙ HGNC:29675 ∙ Uniprot:Q96S66 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

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 (421 variants)
• Chudley-McCullough syndrome (70 variants)
• not specified (49 variants)
• Inborn genetic diseases (47 variants)
• Rare genetic deafness (5 variants)
• Nonsyndromic Hearing Loss, Recessive (3 variants)
• GPSM2-Related Disorders (3 variants)
• Retinitis pigmentosa 32 (2 variants)
• Hearing loss, autosomal recessive (2 variants)
• Hearing impairment (1 variants)
• See cases (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.

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	64	5	72
missense	1		124	4	6	135
nonsense			4			4
start loss						0
frameshift			10			10
inframe indel			2			2
splice donor/acceptor (+/-2bp)			6	1		7
splice region			5	10	1	16
non coding	10	16	105	76	28	235
Total	11	16	254	145	39

Highest pathogenic variant AF is 0.0000592

Variants in CLCC1

This is a list of pathogenic ClinVar variants found in the CLCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108885096-C-G			Likely benign (Aug 17, 2018)
1-108885259-T-C		not specified	Likely benign (Feb 04, 2016)
1-108885274-G-A		Chudley-McCullough syndrome	Uncertain significance (Aug 22, 2018)
1-108885278-T-A		Chudley-McCullough syndrome	Uncertain significance (Jan 13, 2018)
1-108885521-C-T		not specified	Uncertain significance (Sep 03, 2013)
1-108885533-A-T		Chudley-McCullough syndrome	Likely benign (Mar 29, 2024)
1-108885545-T-C			Uncertain significance (Sep 30, 2019)
1-108885558-T-C			Uncertain significance (Dec 28, 2022)
1-108885572-G-A			Uncertain significance (Sep 18, 2021)
1-108885627-G-A			Benign (Jun 24, 2018)
1-108885722-G-GT			Benign (Mar 29, 2019)
1-108885733-T-C			Likely benign (Oct 28, 2018)
1-108896740-C-T			Benign (Jul 15, 2018)
1-108896778-C-T			Benign (Jun 30, 2018)
1-108896854-A-G		not specified • GPSM2-related disorder	Conflicting classifications of pathogenicity (Dec 19, 2023)
1-108896894-G-A		not specified • Chudley-McCullough syndrome	Benign/Likely benign (Jan 26, 2024)
1-108896928-C-T			Uncertain significance (Nov 27, 2023)
1-108896930-C-T		not specified	Likely benign (Oct 26, 2015)
1-108896931-G-A		Chudley-McCullough syndrome	Uncertain significance (Aug 07, 2018)
1-108896936-C-T			Uncertain significance (Aug 26, 2019)
1-108896937-G-C		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
1-108896945-C-A		Deafness • Hearing loss, autosomal recessive	Pathogenic/Likely pathogenic (Sep 10, 2018)
1-108896979-C-T		not specified	Likely benign (Feb 09, 2023)
1-108896993-C-T		not specified • Chudley-McCullough syndrome	Conflicting classifications of pathogenicity (Mar 01, 2024)
1-108897045-A-G			Uncertain significance (Oct 24, 2022)

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
• 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