CSAG1

Chr X

chondrosarcoma associated gene 1

Also known as: CSAGE, CT24.1

NCBI Gene: 158511ENSG00000198930UniProt: Q6PB30

This gene encodes a member of a family of tumor antigens. The protein is expressed in chondrosarcomas, but may also be expressed in normal tissues such as testis. Alternative splicing of this gene results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

117
ClinVar variants
88
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— CSAG1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
88 Pathogenic / Likely Pathogenic· 25 VUS of 117 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.92LOEUF
pLI 0.004
Z-score -0.57
OE 1.42 (0.55–1.92)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-1.04Z-score
OE missense 1.54 (1.21–1.90)
45 obs / 29.2 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.1.42 (0.55–1.92)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.54 (1.21–1.90)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.77
0≤1.21.6
LoF obs/exp: 3 / 2.1Missense obs/exp: 45 / 29.2Syn Z: -2.09

ClinVar Variant Classifications

117 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic86
Likely Pathogenic2
VUS25
Likely Benign3
Benign1
86
Pathogenic
2
Likely Pathogenic
25
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
86
0
86
Likely Pathogenic
0
0
2
0
2
VUS
0
15
10
0
25
Likely Benign
0
2
1
0
3
Benign
0
1
0
0
1
Total018990117

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CSAG1 · 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
Differential gene expression and network analysis in head and neck squamous cell carcinoma.
Habib I et al.·Mol Cell Biochem
2022
Causal effect of gut microbiota metabolic pathways on CSAG1 expression in chondrosarcoma: a mendelian randomization analysis.
Liu X et al.·BMC Cancer
2025
Gastric cancer metastasis-related NT5DC2 indicates unfavorable prognosis of patients.
Sha R et al.·Medicine (Baltimore)
2023Cohort
CSAG1 maintains the integrity of the mitotic centrosome in cells with defective p53.
Sapkota H et al.·J Cell Sci
2020
An ensemble method integrated with miRNA expression data for predicting miRNA targets in stomach adenocarcinoma.
Liu GW et al.·Cancer Biomark
2017
Chimeric transcripts resulting from complex duplications in chromosome Xq28.
Zuccherato LW et al.·Hum Genet
2016
Exome sequencing in a family segregating for celiac disease.
Szperl AM et al.·Clin Genet
2011
A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family.
Hansen MA et al.·Mol Reprod Dev
2008
An integrative analysis of GEO data to identify possible therapeutic biomarkers of prostate cancer and targeting potential protein through Zea mays phytochemicals by virtual screening approaches.
Modanwal S et al.·J Biomol Struct Dyn
2025
Cancer/testis antigen CSAGE is concurrently expressed with MAGE in chondrosarcoma.
Lin C et al.·Gene
2002
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools