CAGE1

cancer antigen 1

Basic information

Region (hg38): 6:7326656-7389742

Previous symbols: [ "CTAG3" ]

Links

ENSG00000164304 ∙ NCBI:285782 ∙ OMIM:608304 ∙ HGNC:21622 ∙ Uniprot:Q8TC20 ∙ 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 CAGE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CAGE1 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			37	3		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	38	4	0

Variants in CAGE1

This is a list of pathogenic ClinVar variants found in the CAGE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-7329185-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-7329855-C-G		not specified	Uncertain significance (Apr 22, 2022)
6-7329865-G-A		not specified	Uncertain significance (Oct 29, 2021)
6-7334072-T-G		not specified	Uncertain significance (Sep 16, 2021)
6-7334088-A-C		not specified	Uncertain significance (Jul 30, 2024)
6-7355060-A-G		not specified	Uncertain significance (Nov 27, 2024)
6-7355061-T-C		not specified	Uncertain significance (Jul 13, 2022)
6-7355089-A-G		not specified	Uncertain significance (Oct 12, 2021)
6-7355101-T-C		not specified	Uncertain significance (May 31, 2023)
6-7356075-T-C		not specified	Uncertain significance (Nov 11, 2024)
6-7356086-C-T		not specified	Uncertain significance (Aug 09, 2021)
6-7365478-A-G		not specified	Uncertain significance (Jul 20, 2021)
6-7365494-T-G		not specified	Uncertain significance (Jun 05, 2024)
6-7365571-A-G		not specified	Likely benign (Sep 03, 2024)
6-7365809-T-C		not specified	Uncertain significance (Jul 19, 2022)
6-7365869-C-A		not specified	Uncertain significance (Jan 04, 2024)
6-7369956-C-G		not specified	Uncertain significance (Dec 21, 2023)
6-7369980-G-T		not specified	Uncertain significance (Feb 22, 2023)
6-7370034-G-A		not specified	Likely benign (Dec 13, 2023)
6-7370059-T-C		not specified	Uncertain significance (Jul 10, 2024)
6-7373123-C-T		not specified	Uncertain significance (Jun 18, 2024)
6-7373128-T-A		not specified	Uncertain significance (May 14, 2024)
6-7373173-T-C		not specified	Uncertain significance (Sep 21, 2023)
6-7373236-G-A		not specified	Uncertain significance (Oct 01, 2024)
6-7373296-C-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CAGE1	protein_coding	protein_coding	ENST00000502583	13	63088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.71e-14	0.653	124596	0	39	124635	0.000156

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.886	339	388	0.873	0.0000179	5619
Missense in Polyphen		137	167.85	0.81622		2652
Synonymous	-0.782	150	138	1.08	0.00000690	1396
Loss of Function	1.67	26	36.9	0.704	0.00000164	555

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000223
Ashkenazi Jewish	0.0000997	0.0000994
East Asian	0.000224	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000177
Middle Eastern	0.000224	0.000223
South Asian	0.000330	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0770

Intolerance Scores

• loftool: 0.899
• rvis_EVS: 1.02
• rvis_percentile_EVS: 91.02

Haploinsufficiency Scores

• pHI: 0.0311
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cage1

Gene ontology

• Molecular function: protein binding