CTAGE1

protein-coding

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

Gene summary

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport; protein secretion; and vesicle cargo loading. Predicted to be located in membrane. Predicted to be active in endoplasmic reticulum exit site and endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_172241.3

Inheritance

—

ClinVar variants

U:136B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chr18:22,413,599-22,417,915

External References & Databases

Ensembl (ENSG00000212710)

UniProt (Q96RT6, Q9HC47)

Transcript & Mutation Effects

hg38 • Region Span ~4.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CTAGE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 146

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_172241.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			136 clinvar	10 clinvar	4 clinvar	150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	136	11	5	152

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_172241.3	RefSeq	NP_758441.2	1	MANE Select
ENST00000391403.4	Ensembl	ENSP00000375220.2	1	MANE Select
ENST00000525417.1	Ensembl	ENSP00000436900.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
biological_process
protein secretion
vesicle cargo loading
lipoprotein transport

Molecular Function

lipoprotein transporter activity

Cellular Component

cellular_component
endoplasmic reticulum membrane
integral component of membrane
endoplasmic reticulum exit site

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000391403
Coding exons: 1
Length: 4315

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.920
RVIS EVS: -0.26
RVIS percentile EVS: 34.95

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.142

Gene Damage Prediction

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