CLTA

clathrin light chain A, the group of Clathrin subunits

Basic information

Region (hg38): 9:36190855-36304781

Links

ENSG00000122705 ∙ NCBI:1211 ∙ OMIM:118960 ∙ HGNC:2090 ∙ Uniprot:P09496 ∙ 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 CLTA gene.

• Inborn genetic diseases (13 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLTA 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					1	1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	13	0	1

Variants in CLTA

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

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

Position	Type	Phenotype	Significance	ClinVar
9-36191078-G-C		not specified	Uncertain significance (Sep 27, 2021)
9-36191096-C-G		not specified	Uncertain significance (Aug 30, 2021)
9-36191108-G-A		not specified	Uncertain significance (Sep 06, 2022)
9-36191208-C-T		not specified	Uncertain significance (Sep 30, 2021)
9-36191268-G-T		not specified	Uncertain significance (Dec 21, 2022)
9-36198973-G-A			Benign (Dec 31, 2019)
9-36199012-A-G		not specified	Uncertain significance (May 04, 2023)
9-36199028-G-A		not specified	Uncertain significance (Feb 27, 2023)
9-36199035-G-C		not specified	Uncertain significance (Aug 02, 2021)
9-36204079-C-T		not specified	Uncertain significance (Apr 05, 2023)
9-36204081-G-A			Benign (Dec 31, 2019)
9-36204114-A-G		not specified	Uncertain significance (Jun 21, 2023)
9-36209319-G-A		not specified	Uncertain significance (May 17, 2023)
9-36210632-A-G		not specified	Uncertain significance (Apr 18, 2023)
9-36211614-A-C		not specified	Uncertain significance (Sep 29, 2022)
9-36211653-C-T		not specified	Uncertain significance (Feb 12, 2024)
9-36214458-ATT-A		Sialuria • GNE myopathy • Inclusion Body Myopathy, Recessive	Uncertain significance (Jun 14, 2016)
9-36214488-A-G		GNE myopathy • Inclusion Body Myopathy, Recessive • Sialuria	Uncertain significance (Jan 12, 2018)
9-36214518-A-G		GNE myopathy • Inclusion Body Myopathy, Recessive • Sialuria	Uncertain significance (Jan 13, 2018)
9-36214576-C-T		Sialuria • GNE myopathy • Inclusion Body Myopathy, Recessive	Benign/Likely benign (Jan 13, 2018)
9-36214599-A-G		Inclusion Body Myopathy, Recessive • Sialuria • GNE myopathy	Uncertain significance (Jan 13, 2018)
9-36214656-A-G		Sialuria • GNE myopathy	Uncertain significance (Jan 12, 2018)
9-36214686-C-T		Inclusion Body Myopathy, Recessive • Sialuria • GNE myopathy	Uncertain significance (Jan 13, 2018)
9-36214789-T-C		Sialuria • Inclusion Body Myopathy, Recessive • GNE myopathy	Likely benign (Apr 27, 2017)
9-36214815-C-T		GNE myopathy • Sialuria	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLTA	protein_coding	protein_coding	ENST00000242285	7	113926

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0368	125570	0	2	125572	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.799	117	144	0.813	0.00000803	1607
Missense in Polyphen		25	52.997	0.47173		618
Synonymous	0.0995	53	53.9	0.983	0.00000301	464
Loss of Function	3.31	1	14.7	0.0681	6.92e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000616
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000982	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Acts as component of the TACC3/ch- TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter- microtubule bridge (PubMed:15858577, PubMed:21297582). {ECO:0000305|PubMed:15858577, ECO:0000305|PubMed:21297582}.
• 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);Synaptic Vesicle Pathway;Developmental Biology;Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;Signaling by WNT;Signal Transduction;Recycling pathway of L1;Vesicle-mediated transport;Membrane Trafficking;Entry of Influenza Virion into Host Cell via Endocytosis;Influenza Life Cycle;Influenza Infection;MHC class II antigen presentation;Infectious disease;Immune System;LDL clearance;VLDLR internalisation and degradation;Plasma lipoprotein clearance;Adaptive Immune System;Retrograde neurotrophin signalling;Transport of small molecules;adp-ribosylation factor;Clathrin-mediated endocytosis;Signaling by NTRK1 (TRKA);WNT5A-dependent internalization of FZD4;PCP/CE pathway;Signaling by NTRKs;EGFR1;Beta-catenin independent WNT signaling;Arf1 pathway;C-MYB transcription factor network;Plasma lipoprotein assembly, remodeling, and clearance;Cargo recognition for clathrin-mediated endocytosis;L1CAM interactions;Axon guidance;Signaling by Receptor Tyrosine Kinases;Formation of annular gap junctions;Gap junction degradation;Gap junction trafficking;Gap junction trafficking and regulation (Consensus)

Recessive Scores

• pRec: 0.356

Intolerance Scores

• loftool: 0.0255
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.775
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.453

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clta

Gene ontology

• Biological process: intracellular protein transport;cell cycle;antigen processing and presentation of exogenous peptide antigen via MHC class II;low-density lipoprotein particle receptor catabolic process;low-density lipoprotein particle clearance;clathrin coat assembly;cell division;membrane organization;clathrin-dependent endocytosis
• Cellular component: spindle;cytosol;plasma membrane;membrane;clathrin coat;clathrin vesicle coat;clathrin coat of trans-Golgi network vesicle;clathrin coat of coated pit;synaptic vesicle membrane;cytoplasmic vesicle;trans-Golgi network membrane;endolysosome membrane;clathrin-coated endocytic vesicle;clathrin complex;presynaptic endocytic zone membrane;postsynaptic endocytic zone cytoplasmic component
• Molecular function: molecular_function;structural molecule activity;protein binding;clathrin heavy chain binding;peptide binding;protein-containing complex binding;GTPase binding