CTAGE1

cutaneous T cell lymphoma-associated antigen 1, the group of CTAGE family

Basic information

Region (hg38): 18:22413599-22417915

Links

ENSG00000212710 ∙ NCBI:64693 ∙ OMIM:608856 ∙ HGNC:24346 ∙ Uniprot:Q96RT6, Q9HC47 ∙ 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 CTAGE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTAGE1 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	2
missense			71	7	4	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	71	8	5

Variants in CTAGE1

This is a list of pathogenic ClinVar variants found in the CTAGE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-22415581-G-A		not specified	Uncertain significance (Jun 02, 2023)
18-22415585-G-A		not specified	Uncertain significance (Apr 08, 2024)
18-22415615-G-A		not specified	Uncertain significance (Jan 25, 2024)
18-22415615-G-T		not specified	Uncertain significance (Feb 28, 2023)
18-22415656-A-G		not specified	Uncertain significance (Nov 09, 2021)
18-22415690-C-T		not specified	Uncertain significance (Oct 29, 2024)
18-22415699-A-G		not specified	Likely benign (Dec 21, 2022)
18-22415707-T-C		not specified	Uncertain significance (Feb 10, 2025)
18-22415710-G-C		not specified	Likely benign (Dec 21, 2022)
18-22415726-C-T			Benign (Dec 31, 2019)
18-22415734-G-A		not specified	Uncertain significance (Jan 01, 2025)
18-22415746-G-A		not specified	Uncertain significance (Oct 06, 2024)
18-22415756-G-T			Benign (Dec 31, 2019)
18-22415766-T-C			Benign (Apr 20, 2018)
18-22415773-G-A		not specified	Uncertain significance (Jul 30, 2024)
18-22415782-G-A		not specified	Uncertain significance (Aug 02, 2021)
18-22415788-A-C		not specified	Uncertain significance (Sep 02, 2024)
18-22415797-A-C		not specified	Uncertain significance (Feb 08, 2025)
18-22415800-A-G		not specified	Uncertain significance (Aug 12, 2021)
18-22415805-T-G		not specified	Uncertain significance (Feb 22, 2025)
18-22415810-T-A		not specified	Uncertain significance (Nov 05, 2021)
18-22415810-T-C		not specified	Uncertain significance (Dec 01, 2022)
18-22415813-G-A		not specified	Uncertain significance (Aug 12, 2021)
18-22415831-C-T		not specified	Likely benign (Oct 10, 2023)
18-22415834-A-G		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTAGE1	protein_coding	protein_coding	ENST00000391403	1	4315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.67	520	375	1.39	0.0000194	4886
Missense in Polyphen		84	66.647	1.2604		1075
Synonymous	-1.80	163	136	1.20	0.00000745	1416
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.920
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.95

Haploinsufficiency Scores

• pHI: 0.00861
• hipred: N
• hipred_score: 0.112
• ghis: 0.383

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.142

Gene Damage Prediction

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

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;biological_process;protein secretion;vesicle cargo loading;lipoprotein transport
• Cellular component: cellular_component;endoplasmic reticulum membrane;integral component of membrane;endoplasmic reticulum exit site
• Molecular function: lipoprotein transporter activity