CLTB

clathrin light chain B, the group of Clathrin subunits

Basic information

Region (hg38): 5:176392501-176416539

Links

ENSG00000175416 ∙ NCBI:1212 ∙ OMIM:118970 ∙ HGNC:2091 ∙ Uniprot:P09497 ∙ 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 CLTB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLTB 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in CLTB

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

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

Position	Type	Phenotype	Significance	ClinVar
5-176392818-G-A		not specified	Uncertain significance (Jan 20, 2025)
5-176392878-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-176392929-A-G		not specified	Uncertain significance (Jan 19, 2025)
5-176397608-G-A		not specified	Uncertain significance (Apr 06, 2024)
5-176397647-G-A		not specified	Uncertain significance (Feb 13, 2025)
5-176397700-G-A		not specified	Uncertain significance (Nov 09, 2024)
5-176397945-G-A		not specified	Uncertain significance (Nov 10, 2024)
5-176397962-C-T		not specified	Uncertain significance (Aug 26, 2024)
5-176397971-C-T		not specified	Uncertain significance (Feb 27, 2023)
5-176398023-A-G		not specified	Uncertain significance (Jan 26, 2022)
5-176410288-A-C		not specified	Uncertain significance (Nov 25, 2024)
5-176416218-C-G		not specified	Uncertain significance (Aug 12, 2024)
5-176416270-C-G		not specified	Uncertain significance (Apr 25, 2022)
5-176416303-C-G		not specified	Uncertain significance (Mar 31, 2023)
5-176416317-G-A		not specified	Uncertain significance (Apr 14, 2022)
5-176416320-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-176416335-G-C		not specified	Uncertain significance (Feb 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLTB	protein_coding	protein_coding	ENST00000310418	6	24115

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.334	0.663	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	106	140	0.757	0.00000859	1504
Missense in Polyphen		42	61.475	0.6832		636
Synonymous	0.881	47	55.3	0.849	0.00000317	423
Loss of Function	2.56	3	12.9	0.232	6.47e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000193	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Endocytosis - Homo sapiens (human);Lysosome - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Signaling by WNT;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;adp-ribosylation factor;Clathrin-mediated endocytosis;WNT5A-dependent internalization of FZD4;PCP/CE pathway;Beta-catenin independent WNT signaling;Arf1 pathway;Cargo recognition for clathrin-mediated endocytosis;Formation of annular gap junctions;Gap junction degradation;Gap junction trafficking;Gap junction trafficking and regulation (Consensus)

Recessive Scores

• pRec: 0.246

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.586
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.584

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cltb

Gene ontology

• Biological process: intracellular protein transport;clathrin coat assembly;membrane organization;clathrin-dependent endocytosis
• Cellular component: trans-Golgi network;cytosol;plasma membrane;clathrin coat;clathrin vesicle coat;clathrin coat of trans-Golgi network vesicle;clathrin coat of coated pit;synaptic vesicle membrane;intracellular membrane-bounded organelle;clathrin-coated endocytic vesicle;ciliary membrane;presynaptic endocytic zone membrane;postsynaptic endocytic zone cytoplasmic component
• Molecular function: structural molecule activity;protein binding;clathrin heavy chain binding;peptide binding