CT55

protein-coding

cancer/testis antigen 55

Gene summary

Involved in spermatogenesis. Located in acrosomal vesicle and sperm flagellum. Implicated in X-linked spermatogenic failure 7. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CXorf48

MANE transcript

NM_001031705.3

Inheritance

ClinVar variants

P:1U:11B:1

Top phenotype

Spermatogenic failure, X-linked, 7

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chrX:135,156,540-135,171,398

External References & Databases

Ensembl (ENSG00000169551)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failure, X-linked, 7LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0957202

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Spermatogenic failure, X-linked, 7XL

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 36481789

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CT55 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

Spermatogenic failure, X-linked, 7Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031705.3. 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						0
missense			11 clinvar	1 clinvar		12
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	11	1	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031705.3	RefSeq	NP_001026875.1	6	MANE Select
ENST00000276241.11	Ensembl	ENSP00000276241.6	6	MANE Select
NM_017863.2	RefSeq	NP_060333.1	5	Standard
ENST00000344129.2	Ensembl	ENSP00000343893.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000276241
Coding exons: 6
Length: 14862
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.842	43	61.6	0.698	0.00000451	1714
Missense (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

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

Essentials

Essential (gene trap): N

Gene Damage Prediction

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