CLC

Charcot-Leyden crystal galectin, the group of Galectins

Basic information

Region (hg38): 19:39731255-39738029

Links

ENSG00000105205 ∙ NCBI:1178 ∙ OMIM:153310 ∙ HGNC:2014 ∙ Uniprot:Q05315 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLC 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						0
missense			4		1	5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in CLC

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

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

Position	Type	Phenotype	Significance	ClinVar
19-39731420-A-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
19-39731495-T-C		not specified	Uncertain significance (Oct 09, 2024)
19-39731505-C-A		not specified	Uncertain significance (Apr 14, 2022)
19-39734314-A-G		not specified	Uncertain significance (Nov 14, 2023)
19-39734391-G-C			Benign (Apr 27, 2020)
19-39734407-C-T		not specified	Uncertain significance (Jul 19, 2023)
19-39734465-G-A		not specified	Uncertain significance (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLC	protein_coding	protein_coding	ENST00000221804	4	6779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000230	0.309	125677	0	28	125705	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0228	75	75.6	0.993	0.00000383	931
Missense in Polyphen		21	24.269	0.8653		339
Synonymous	-0.804	32	26.7	1.20	0.00000116	257
Loss of Function	0.00152	7	7.00	0.999	4.82e-7	65

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000490	0.000489
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates immune responses through the recognition of cell-surface glycans. Essential for the anergy and suppressive function of CD25-positive regulatory T-cells (Treg). {ECO:0000269|PubMed:17502455}.

Recessive Scores

• pRec: 0.0878

Intolerance Scores

• loftool: 0.712
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• pHI: 0.0431
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0622

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of T cell anergy;regulation of T cell cytokine production;multicellular organism development;regulation of activated T cell proliferation;T cell apoptotic process
• Cellular component: cytosol;collagen-containing extracellular matrix
• Molecular function: lysophospholipase activity;protein binding;carbohydrate binding;identical protein binding;cysteine-type endopeptidase activity involved in apoptotic process