SPANXA2

Chr X

SPANX family member A2

Also known as: CT11.1, SPANX, SPANX-A, SPANXA

NCBI Gene: 728712ENSG00000203926UniProt: Q9NS26

Temporally regulated transcription and translation of several testis-specific genes is required to initiate the series of molecular and morphological changes in the male germ cell lineage necessary for the formation of mature spermatozoa. This gene is a member of the SPANX family of cancer/testis-associated genes, which are located in a cluster on chromosome X. The SPANX genes encode differentially expressed testis-specific proteins that localize to various subcellular compartments. This particular gene maps to chromosome X in a head-to-head orientation with SPANX family member A1 and appears to be a duplication of that locus. The protein encoded by this gene targets to the nucleus where it associates with nuclear vacuoles and the redundant nuclear envelope. Based on its association with these poorly characterized regions of the sperm nucleus, this protein provides a biochemical marker to study unique structures in spermatazoa while attempting to further define its role in spermatogenesis. [provided by RefSeq, Jul 2008]

99
ClinVar variants
87
Pathogenic / LP
—
pLI score
0
Active trials
Clinical Summary— SPANXA2
📋
ClinVar Variants
87 Pathogenic / Likely Pathogenic· 11 VUS of 99 total submissions

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

ClinVar Variant Classifications

99 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic84
Likely Pathogenic3
VUS11
Likely Benign1
84
Pathogenic
3
Likely Pathogenic
11
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
————84
Likely Pathogenic
————3
VUS
————11
Likely Benign
————1
Benign
————0
Total—99

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SPANXA2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
A systems approach to target discovery identifies the role of lncRNA-SPANXA2-OT1 in macrophage chemotaxis.
Jha PK et al.·JCI Insight
2025
Hominoid-specific SPANXA/D genes demonstrate differential expression in individuals and protein localization to a distinct nuclear envelope domain during spermatid morphogenesis.
Westbrook VA et al.·Mol Hum Reprod
2006
Hypomethylated SPANXA1/A2 promotes the metastasis of head and neck squamous cell carcinoma.
Li J et al.·Med Oncol
2020
Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27.
Kouprina N et al.·Genome Res
2005
Mutational analysis of SPANX genes in families with X-linked prostate cancer.
Kouprina N et al.·Prostate
2007
Genomic organization, incidence, and localization of the SPAN-x family of cancer-testis antigens in melanoma tumors and cell lines.
Westbrook VA et al.·Clin Cancer Res
2004
Xq;autosome translocation in POF: Xq27.2 deletion resulting in haploinsufficiency for SPANX.
Vitek WS et al.·J Assist Reprod Genet
2012Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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External Resources

Links to major genomics databases and tools