CTAG2

cancer/testis antigen 2

Basic information

Region (hg38): X:154651972-154653579

Links

ENSG00000126890 ∙ NCBI:30848 ∙ OMIM:300396 ∙ HGNC:2492 ∙ Uniprot:O75638 ∙ 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 CTAG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTAG2 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				2	1	3
missense			23	2	5	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	4	6

Variants in CTAG2

This is a list of pathogenic ClinVar variants found in the CTAG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154652203-A-G			Likely benign (Dec 01, 2022)
X-154652295-A-G			Likely benign (Apr 19, 2018)
X-154652306-C-T		not specified	Uncertain significance (Dec 06, 2022)
X-154652360-C-G			Benign (Apr 19, 2018)
X-154652379-C-A		not specified	Uncertain significance (Feb 06, 2025)
X-154652390-G-T		not specified	Uncertain significance (Jan 08, 2025)
X-154652416-C-T		not specified	Uncertain significance (Apr 20, 2024)
X-154652437-A-G		not specified	Uncertain significance (Dec 02, 2024)
X-154652455-C-T		not specified	Uncertain significance (Jun 22, 2023)
X-154652462-G-A		not specified	Uncertain significance (Apr 07, 2022)
X-154652476-C-G		not specified	Uncertain significance (Mar 28, 2024)
X-154652519-C-T		not specified	Uncertain significance (Aug 22, 2023)
X-154652556-C-A			Benign (May 16, 2018)
X-154652557-G-A		not specified	Uncertain significance (Feb 16, 2023)
X-154652561-C-T		not specified	Likely benign (Jul 12, 2022)
X-154652573-A-C		not specified	Uncertain significance (Feb 08, 2025)
X-154652606-G-C			Benign (May 15, 2018)
X-154652621-T-C			Benign (Apr 30, 2018)
X-154653251-C-G			Benign (Aug 16, 2017)
X-154653266-C-G		not specified	Uncertain significance (Feb 02, 2025)
X-154653298-T-C		not specified	Uncertain significance (Aug 01, 2022)
X-154653317-C-T		not specified	Likely benign (Feb 12, 2025)
X-154653325-G-A		not specified	Uncertain significance (Nov 26, 2024)
X-154653334-G-A		not specified	Uncertain significance (Mar 16, 2022)
X-154653334-G-C		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTAG2	protein_coding	protein_coding	ENST00000247306	2	1608

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.105	0.605	119289	0	1	119290	0.00000419

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.490	119	105	1.13	0.00000987	1306
Missense in Polyphen		13	12.647	1.0279		139
Synonymous	0.338	50	53.1	0.941	0.00000556	496
Loss of Function	0.225	1	1.27	0.785	8.06e-8	24

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000534	0.0000334
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.800
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.44

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.112
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00945

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: centrosome
• Molecular function: molecular_function;protein binding