CT55

cancer/testis antigen 55

Basic information

Region (hg38): X:135156540-135171398

Previous symbols: [ "CXorf48" ]

Links

ENSG00000169551 ∙ NCBI:54967 ∙ ∙ HGNC:26047 ∙ Uniprot:Q8WUE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure, X-linked, 7 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked, 7	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	36481789

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CT55 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CT55 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						0
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in CT55

This is a list of pathogenic ClinVar variants found in the CT55 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-135158240-C-A		not specified	Uncertain significance (Dec 12, 2023)
X-135158240-C-T		not specified	Uncertain significance (May 20, 2024)
X-135158255-T-A		not specified	Uncertain significance (Jun 11, 2021)
X-135158271-A-T		Spermatogenic failure, X-linked, 7	Pathogenic (Sep 27, 2023)
X-135158282-C-T		not specified	Uncertain significance (Sep 06, 2022)
X-135160540-G-A		not specified	Uncertain significance (Sep 22, 2022)
X-135169761-T-C		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CT55	protein_coding	protein_coding	ENST00000276241	6	14862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.485	0.495	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.842	43	61.6	0.698	0.00000451	1714
Missense in Polyphen		3	7.8797	0.38073		329
Synonymous	-0.426	27	24.3	1.11	0.00000199	521
Loss of Function	1.87	1	5.91	0.169	4.44e-7	143

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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0385
• hipred: N
• hipred_score: 0.173

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein binding