CSAG1

Summary

CSAG1 (chondrosarcoma associated gene 1, HGNC:24294) is a protein-coding gene on chromosome Xq28, encoding Chondrosarcoma-associated gene 1 protein (Q6PB30). May play an important role in maintaining centrosome integrity during mitosis.

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.

Source: NCBI Gene 158511 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 22 total — 1 pathogenic
• MANE Select transcript: NM_001102576

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24294
Approved symbol	CSAG1
Name	chondrosarcoma associated gene 1
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	CSAGE, CT24.1
Ensembl gene	ENSG00000198930
Ensembl biotype	protein_coding
OMIM	300944
Entrez	158511

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 nonsense_mediated_decay

ENST00000361211, ENST00000370287, ENST00000370291, ENST00000452779, ENST00000906181, ENST00000930660

RefSeq mRNA: 2 — MANE Select: NM_001102576 NM_001102576, NM_153478

CCDS: CCDS76047

Canonical transcript exons

ENST00000452779 — 4 exons

Exon	Start	End
ENSE00001718327	152728074	152728224
ENSE00001894127	152733668	152733721
ENSE00002159992	152732445	152732504
ENSE00003551347	152727484	152727863

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 86.17.

FANTOM5 (CAGE): breadth broad, TPM avg 3.9717 / max 116.5343, expressed in 221 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200849	1.8227	182
200851	1.5285	180
200850	0.6205	163

Top tissues by expression

117 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.17	gold quality
putamen	UBERON:0001874	64.64	gold quality
amygdala	UBERON:0001876	63.64	gold quality
temporal lobe	UBERON:0001871	63.11	gold quality
caudate nucleus	UBERON:0001873	62.77	gold quality
Ammon’s horn	UBERON:0001954	62.25	gold quality
substantia nigra	UBERON:0002038	61.79	gold quality
anterior cingulate cortex	UBERON:0009835	61.62	gold quality
apex of heart	UBERON:0002098	60.42	gold quality
superior frontal gyrus	UBERON:0002661	59.91	gold quality
nucleus accumbens	UBERON:0001882	59.29	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	59.28	gold quality
cerebral cortex	UBERON:0000956	58.35	gold quality
right frontal lobe	UBERON:0002810	57.52	gold quality
hypothalamus	UBERON:0001898	56.48	gold quality
frontal cortex	UBERON:0001870	56.41	gold quality
lymph node	UBERON:0000029	55.65	gold quality
prefrontal cortex	UBERON:0000451	55.46	gold quality
Brodmann (1909) area 9	UBERON:0013540	54.91	gold quality
primary visual cortex	UBERON:0002436	54.36	gold quality
brain	UBERON:0000955	54.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	53.97	gold quality
testis	UBERON:0000473	51.86	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	51.58	gold quality
left testis	UBERON:0004533	50.94	gold quality
right testis	UBERON:0004534	50.90	gold quality
right hemisphere of cerebellum	UBERON:0014890	47.37	gold quality
cerebellar hemisphere	UBERON:0002245	46.56	gold quality
cerebellum	UBERON:0002037	46.52	gold quality
cerebellar cortex	UBERON:0002129	46.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.13

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• CSAG1 maintains the integrity of the mitotic centrosome in cells with defective p53. (PMID:32295846)

Cross-species orthologs

0 orthologs

Paralogs (2): CSAG2 (ENSG00000268902), CSAG3 (ENSG00000268916)

Protein

Protein identifiers

Chondrosarcoma-associated gene 1 protein — Q6PB30 (reviewed: Q6PB30)

Alternative names: Cancer/testis antigen 24.1, Cancer/testis antigen CSAGE

All UniProt accessions (2): Q6PB30, H9KV60

UniProt curated annotations — full annotation on UniProt →

Function. May play an important role in maintaining centrosome integrity during mitosis.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Spindle pole.

Tissue specificity. Expressed in chondrosarcoma, melanoma, cartilage and testis, but not in other normal tissues.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PB30-1	1, CSAG1a	yes
Q6PB30-2	2, CSAG1c

RefSeq proteins (2): NP_001096046, NP_705611 (=MANE)

Domains & families (InterPro)

UniProt features (7 total): sequence variant 2, signal peptide 1, chain 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PB30-F1	63.01	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_CENTROSOME, GOCC_SPINDLE, GOBP_CELL_CYCLE_PROCESS, chrXq28, GOBP_MICROTUBULE_CYTOSKELETON_ORGANIZATION, GOBP_MICROTUBULE_ORGANIZING_CENTER_ORGANIZATION, ZNF184_TARGET_GENES, MIR3942_3P, MIR6853_3P, MIR661, MIR6819_5P, MIR6737_5P, MIR652_3P, FAN_EMBRYONIC_CTX_BRAIN_ENDOTHELIAL_2

GO Biological Process (1): centrosome cycle (GO:0007098)

GO Molecular Function (0):

GO Cellular Component (4): spindle pole (GO:0000922), centrosome (GO:0005813), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell cycle process	1
microtubule organizing center organization	1
spindle	1
centriole	1
microtubule organizing center	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSAG1	MAGEF1	Q9HAY2	824
CSAG1	NPAS4	Q8IUM7	818
CSAG1	NSMCE3	Q96MG7	815
CSAG1	MAGEA3	P43357	806
CSAG1	MAGED2	Q9UNF1	748
CSAG1	MAGEA1	P43355	741
CSAG1	MAGEL2	Q9UJ55	726
CSAG1	MAGEA6	P43360	636
CSAG1	NDN	Q99608	632
CSAG1	MAGEA12	P43365	605
CSAG1	MAGEA2B	P43356	542
CSAG1	AQP7B	A0A075B734	518
CSAG1	MAGEA10	P43363	486
CSAG1	CT45A3	P0DMU6	474
CSAG1	FTHL17	Q9BXU8	448

IntAct

5 interactions, top by confidence:

A	B	Type	Score
MAP1LC3A	CSAG1	psi-mi:“MI:0407”(direct interaction)	0.440
CSAG1	SRPK2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
CSAG1	SRPK1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
CSAG1	NAP1L4	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): CSAG1 (Protein-peptide), CSAG1 (Reconstituted Complex), APP (Reconstituted Complex), CSAG1 (Biochemical Activity), CSAG1 (Biochemical Activity)

ESM2 similar proteins: A0A0U1RRE5, A0A1B0GUV1, A5LFY3, A6NEH8, A6NH13, A8MQ11, B0BND4, B1AUF7, B1PS81, B4RE94, P03163, P03294, P03848, P05671, P06925, P06926, P0CU23, P0DPO2, P0DXO0, P11301, P12064, P16817, P17145, P27070, P92563, P93318, Q03352, Q03831, Q0D252, Q3SY05, Q4G0N7, Q54NK2, Q5RDV1, Q5T6M2, Q5TEZ4, Q64202, Q6PB30, Q6RVD6, Q6ZS52, Q7Z2R9

Diamond homologs: Q6PB30, Q9Y5P2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

22 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	15
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
626291	Single allele	Pathogenic

SpliceAI

473 predictions. Top by Δscore:

Variant	Effect	Δscore
X:152732441:T:A	donor_loss	1.0000
X:152732443:GGTAA:G	donor_loss	1.0000
X:152732444:AGGTA:A	donor_loss	1.0000
X:152732445:CAGGT:C	donor_loss	1.0000
X:152732446:ACAG:A	donor_loss	1.0000
X:152732447:TACAG:T	donor_loss	1.0000
X:152732511:A:G	acceptor_gain	1.0000
X:152732512:A:AG	acceptor_gain	1.0000
X:152732513:T:G	acceptor_gain	1.0000
X:152732514:A:AG	acceptor_gain	1.0000
X:152733665:G:GG	donor_gain	1.0000
X:152733665:GTAA:G	donor_loss	1.0000
X:152732503:G:GA	acceptor_gain	0.9900
X:152732503:GG:G	acceptor_gain	0.9900
X:152732503:GGGTT:G	acceptor_gain	0.9900
X:152732504:A:AG	acceptor_gain	0.9900
X:152732504:A:G	acceptor_loss	0.9900
X:152732504:AG:A	acceptor_gain	0.9900
X:152732505:CA:C	acceptor_loss	0.9900
X:152732506:ACAG:A	acceptor_gain	0.9900
X:152732507:TACA:T	acceptor_loss	0.9900
X:152732518:T:G	acceptor_gain	0.9900
X:152733664:T:G	donor_loss	0.9900
X:152733668:GAGG:G	donor_gain	0.9900
X:152733669:GGAG:G	donor_gain	0.9900
X:152733670:TGG:T	donor_gain	0.9900
X:152728938:G:GT	donor_gain	0.9800
X:152732442:G:GG	donor_gain	0.9800
X:152732503:GGGT:G	acceptor_gain	0.9800
X:152732519:A:AG	acceptor_gain	0.9800

AlphaMissense

492 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:152728208:G:C	F11L	0.881
X:152728208:G:T	F11L	0.881
X:152728210:A:G	F11L	0.881
X:152727860:G:C	F57L	0.805
X:152727860:G:T	F57L	0.805
X:152727862:A:G	F57L	0.805
X:152728219:A:G	W8R	0.765
X:152728219:A:T	W8R	0.765
X:152728171:A:G	W24R	0.734
X:152728171:A:T	W24R	0.734
X:152728124:T:A	K39N	0.722
X:152728124:T:G	K39N	0.722
X:152728133:C:A	M36I	0.674
X:152728133:C:G	M36I	0.674
X:152728133:C:T	M36I	0.674
X:152728217:C:A	W8C	0.663
X:152728217:C:G	W8C	0.663
X:152728154:T:A	R29S	0.661
X:152728154:T:G	R29S	0.661
X:152728109:G:C	S44R	0.660
X:152728109:G:T	S44R	0.660
X:152728111:T:G	S44R	0.660
X:152728127:C:A	R38S	0.658
X:152728127:C:G	R38S	0.658
X:152728153:C:G	D30H	0.641
X:152727824:C:A	K69N	0.620
X:152727824:C:G	K69N	0.620
X:152728125:T:A	K39I	0.613
X:152728166:A:C	S25R	0.611
X:152728166:A:T	S25R	0.611

dbSNP variants (sampled 300 via entrez): RS111942589 (X:152733616 G>C,T), RS111946653 (X:152732998 G>C), RS112028367 (X:152727322 G>A), RS112142853 (X:152732819 T>C), RS112210250 (X:152734522 G>A), RS112383352 (X:152732878 T>C,G), RS112479592 (X:152727882 G>A,C,T), RS112733171 (X:152732500 C>G,T), RS11305947 (X:152731726 GA>G,GAA,GAAA), RS11320724 (X:152729524 GA>G), RS113496515 (X:152732541 C>A), RS113546558 (X:152728216 G>A), RS1156431260 (X:152734902 G>A), RS1156642244 (X:152734180 CA>C), RS1156813690 (X:152733707 T>C)

Disease associations

OMIM: gene MIM:300944 | disease phenotypes: MIM:300260

GenCC curated gene-disease

Mondo (1): syndromic X-linked intellectual disability Lubs type (MONDO:0010283)

Orphanet (1): Proximal Xq28 duplication syndrome (Orphanet:1762)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537723	Lubs X-linked mental retardation syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	decreases methylation	1
Cadmium Chloride	increases expression, increases abundance	1

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT03077308	Not specified	COMPLETED	Rare Diseases Clinical Research Network: Neurophysiological Correlates
NCT06615206	Not specified	RECRUITING	A First-in-Human Clinical Trial to Evaluate the Safety, Tolerability, and Efficacy of a Novel CRISPR RNA-editing Therapy in Patients with Mecp2 Duplication Syndrome, a Rare Orphan Disease (HERO)