SSX7

Summary

SSX7 (SSX family member 7, HGNC:19653) is a protein-coding gene on chromosome Xp11.22, encoding Protein SSX7 (Q7RTT5). Could act as a modulator of transcription.

The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneously humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 and SSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. This gene appears not to be involved in this type of chromosome translocation.

Source: NCBI Gene 280658 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_173358

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19653
Approved symbol	SSX7
Name	SSX family member 7
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187754
Ensembl biotype	protein_coding
OMIM	300542
Entrez	280658

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000298181

RefSeq mRNA: 1 — MANE Select: NM_173358 NM_173358

CCDS: CCDS14343

Canonical transcript exons

ENST00000298181 — 8 exons

Exon	Start	End
ENSE00001315615	52654762	52654900
ENSE00001316758	52652870	52652984
ENSE00001674839	52653404	52653492
ENSE00001711712	52650353	52650402
ENSE00001721914	52644061	52644670
ENSE00001729264	52652252	52652347
ENSE00002279637	52645439	52645543
ENSE00002308002	52648261	52648396

Expression profiles

Bgee: expression breadth broad, 22 present calls, max score 49.24.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	49.24	silver quality
right uterine tube	UBERON:0001302	46.09	silver quality
lower esophagus mucosa	UBERON:0035834	44.37	silver quality
ventricular zone	UBERON:0003053	40.36	silver quality
right lung	UBERON:0002167	38.56	silver quality
sural nerve	UBERON:0015488	37.60	gold quality
mucosa of transverse colon	UBERON:0004991	37.54	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
blood	UBERON:0000178	35.48	gold quality
bone marrow	UBERON:0002371	35.35	gold quality
monocyte	CL:0000576	35.06	gold quality
skin of abdomen	UBERON:0001416	34.94	silver quality
esophagus mucosa	UBERON:0002469	34.75	silver quality
mucosa of stomach	UBERON:0001199	34.67	gold quality
liver	UBERON:0002107	34.64	gold quality
adrenal tissue	UBERON:0018303	34.12	gold quality
right lobe of liver	UBERON:0001114	33.69	gold quality
primary visual cortex	UBERON:0002436	33.59	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
zone of skin	UBERON:0000014	33.07	silver quality
rectum	UBERON:0001052	33.01	silver quality
right adrenal gland cortex	UBERON:0035827	32.50	silver quality
ectocervix	UBERON:0012249	32.28	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
urinary bladder	UBERON:0001255	31.37	gold quality
gall bladder	UBERON:0002110	31.27	gold quality
vagina	UBERON:0000996	31.14	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting SSX7, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4697-3P	99.89	67.09	1123
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-12119	99.87	68.35	1653
HSA-MIR-7978	99.86	66.90	856
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-1208	99.70	68.28	1533
HSA-MIR-4261	99.59	70.30	3415
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-147B-5P	99.45	70.62	2432
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-501-3P	99.33	66.12	651
HSA-MIR-502-3P	99.33	66.12	651
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-4641	99.28	66.64	744
HSA-MIR-3160-5P	99.28	69.07	1938
HSA-MIR-5190	99.15	67.76	1234
HSA-MIR-4711-3P	98.97	66.87	1020
HSA-MIR-6871-5P	98.90	66.67	671
HSA-MIR-6804-3P	98.72	64.82	852

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ssxb2	ENSMUSG00000023165
mus_musculus	Ssxb13	ENSMUSG00000035371
mus_musculus	Ssxa1	ENSMUSG00000062814
mus_musculus	Ssxb9	ENSMUSG00000068218
mus_musculus	Ssxb10	ENSMUSG00000068219
mus_musculus	Ssxb5	ENSMUSG00000071816
mus_musculus	Ssxb16	ENSMUSG00000079697
mus_musculus	Ssxb14	ENSMUSG00000079699
mus_musculus	Ssxb3	ENSMUSG00000079701
mus_musculus	Ssxb6	ENSMUSG00000079702
mus_musculus	Ssxb8	ENSMUSG00000079703
mus_musculus	Ssxb15	ENSMUSG00000079704
mus_musculus	Ssxb1	ENSMUSG00000079705
rattus_norvegicus	Ssx1	ENSRNOG00000027850
rattus_norvegicus	Ssx2	ENSRNOG00000049427

Paralogs (7): SSX1 (ENSG00000126752), SSX5 (ENSG00000165583), SSX3 (ENSG00000165584), SSX2 (ENSG00000241476), SSX4 (ENSG00000268009), SSX2B (ENSG00000268447), SSX4B (ENSG00000269791)

Protein

Protein identifiers

Protein SSX7 — Q7RTT5 (reviewed: Q7RTT5)

All UniProt accessions (1): Q7RTT5

UniProt curated annotations — full annotation on UniProt →

Function. Could act as a modulator of transcription.

Tissue specificity. Testis-specific. Expressed in a melanoma cell line.

Similarity. Belongs to the SSX family.

RefSeq proteins (1): NP_775494* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003655	aKRAB	Domain
IPR019041	SSXRD_motif	Conserved_site
IPR036051	KRAB_dom_sf	Homologous_superfamily

Pfam: PF09514

UniProt features (8 total): compositionally biased region 3, chain 1, domain 1, region of interest 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7RTT5-F1	68.62	0.28

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 123

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, OCT1_06, chrXp11, PRDM12_TARGET_GENES, ZNF577_TARGET_GENES, ZNF781_TARGET_GENES, MIR6867_5P, MIR4306, MIR4261, MIR147B_5P, MIR4697_3P, MIR549A_5P, MIR3650, MIR1282, ZNF623_TARGET_GENES

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

142 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSX7	IGSF22	Q8N9C0	584
SSX7	CTAG1A	P78358	492
SSX7	C17orf107	Q6ZR85	480
SSX7	SPANXN4	Q5MJ08	471
SSX7	SPANXN3	Q5MJ09	447
SSX7	SPANXN2	Q5MJ10	430
SSX7	MAGEB6	Q8N7X4	422
SSX7	SPANXN1	Q5VSR9	419
SSX7	ETV3L	Q6ZN32	400
SSX7	XAGE3	Q8WTP9	380
SSX7	GPR82	Q96P67	380
SSX7	MAGEB4	O15481	373
SSX7	ROPN1	Q9HAT0	370
SSX7	A0A1W2PQG5	A0A1W2PQG5	370
SSX7	EPPIN	O95925	368

IntAct

22 interactions, top by confidence:

A	B	Type	Score
DNAAF11	SSX7	psi-mi:“MI:0915”(physical association)	0.560
SSX7	LRRC45	psi-mi:“MI:0915”(physical association)	0.560
	SSX7	psi-mi:“MI:0915”(physical association)	0.560
LRRC45	SSX7	psi-mi:“MI:0915”(physical association)	0.560
SSX7	SERTAD1	psi-mi:“MI:0915”(physical association)	0.560
SSX7	CIB1	psi-mi:“MI:0915”(physical association)	0.560
SSX7	DNAAF11	psi-mi:“MI:0915”(physical association)	0.560
SSX3	CDR2	psi-mi:“MI:0914”(association)	0.530
SSX2	SSX5	psi-mi:“MI:0914”(association)	0.350
SSX3	NCS1	psi-mi:“MI:0914”(association)	0.350
SSX7	DHX32	psi-mi:“MI:0914”(association)	0.350
SSX7	SERTAD1	psi-mi:“MI:0915”(physical association)	0.000
SERTAD1	SSX7	psi-mi:“MI:0915”(physical association)	0.000
SSX7	CIB1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): SSX7 (Affinity Capture-MS), SSX7 (Affinity Capture-MS), SSX7 (Two-hybrid), SSX7 (Two-hybrid), SSX7 (Two-hybrid), SSX7 (Two-hybrid), SERTAD1 (Two-hybrid), MARS2 (Affinity Capture-MS), DHX32 (Affinity Capture-MS), SSX7 (Affinity Capture-MS), WWC1 (Affinity Capture-MS)

ESM2 similar proteins: A6H5X4, B1AUS7, D0QMC3, O35368, O60224, O60225, P0C6Y7, P0DOV1, P0DOV2, P23497, P41218, Q15361, Q16384, Q16385, Q16666, Q2KIN0, Q3U827, Q3ZCI6, Q4R7Q1, Q504N7, Q5H9L4, Q5I0E2, Q5I0J8, Q5RAK3, Q5RCZ8, Q5RD14, Q5W0A0, Q62187, Q6K0P9, Q71F23, Q7RTT3, Q7RTT4, Q7RTT5, Q7RTT6, Q86T96, Q8BV49, Q8BVM9, Q8C0V1, Q8C6C7, Q8CGE8

Diamond homologs: B1AUS7, O60224, O60225, P0C6Y7, Q16384, Q16385, Q7RTT3, Q7RTT4, Q7RTT5, Q7RTT6, Q8BFS8, Q96EQ9, Q99909, Q9NQV7, Q9NQW5, Q6ZMS7, A0A163UT06, A2AGX3, B8A5Y1, E9Q3T6, O75626, P10072, P52736, Q13029, Q14929, Q60636, Q63755, Q6P1L6, Q6P2A1, Q86UQ0, Q8BZ97, Q8TD17, Q9GZV8, Q9NQV5, Q9NQV8, Q9ULD5, Q9Y3M9, A2AJ77, C9JBD0, P14404

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	7
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1358 predictions. Top by Δscore:

Variant	Effect	Δscore
X:52644671:C:CC	acceptor_gain	1.0000
X:52644677:C:CT	acceptor_gain	1.0000
X:52644678:A:T	acceptor_gain	1.0000
X:52645435:TTACG:T	donor_loss	1.0000
X:52645436:T:TG	donor_loss	1.0000
X:52645437:A:AC	donor_gain	1.0000
X:52645438:C:CT	donor_gain	1.0000
X:52645438:CG:C	donor_gain	1.0000
X:52645438:CGG:C	donor_gain	1.0000
X:52645438:CGGA:C	donor_gain	1.0000
X:52645539:GGGTC:G	acceptor_gain	1.0000
X:52645540:GGTC:G	acceptor_gain	1.0000
X:52645541:GTC:G	acceptor_gain	1.0000
X:52645542:TC:T	acceptor_gain	1.0000
X:52645543:CC:C	acceptor_gain	1.0000
X:52645544:C:CC	acceptor_gain	1.0000
X:52645545:T:C	acceptor_loss	1.0000
X:52645549:A:AC	acceptor_gain	1.0000
X:52648399:T:C	acceptor_gain	1.0000
X:52648404:A:AC	acceptor_gain	1.0000
X:52648404:A:C	acceptor_gain	1.0000
X:52648406:G:GC	acceptor_gain	1.0000
X:52650403:C:CC	acceptor_gain	1.0000
X:52651322:CATG:C	donor_gain	1.0000
X:52652895:T:A	donor_gain	1.0000
X:52652913:G:C	donor_gain	1.0000
X:52652985:C:CC	acceptor_gain	1.0000
X:52653398:CCTCA:C	donor_loss	1.0000
X:52653399:CTCA:C	donor_loss	1.0000
X:52653400:TCAC:T	donor_loss	1.0000

AlphaMissense

1267 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:52652958:G:C	F32L	0.910
X:52652958:G:T	F32L	0.910
X:52652960:A:G	F32L	0.910
X:52652322:G:C	F70L	0.904
X:52652322:G:T	F70L	0.904
X:52652324:A:G	F70L	0.904
X:52652898:C:A	K52N	0.868
X:52652898:C:G	K52N	0.868
X:52652943:C:A	W37C	0.867
X:52652943:C:G	W37C	0.867
X:52652979:G:C	F25L	0.849
X:52652979:G:T	F25L	0.849
X:52652981:A:G	F25L	0.849
X:52652945:A:G	W37R	0.808
X:52652945:A:T	W37R	0.808
X:52645497:T:A	R171S	0.799
X:52645497:T:G	R171S	0.799
X:52645467:G:C	S181R	0.791
X:52645467:G:T	S181R	0.791
X:52645469:T:G	S181R	0.791
X:52652885:C:G	A57P	0.739
X:52645471:A:G	I180T	0.726
X:52652934:C:A	M40I	0.724
X:52652934:C:G	M40I	0.724
X:52652934:C:T	M40I	0.724
X:52653452:A:C	F7L	0.722
X:52653452:A:T	F7L	0.722
X:52653454:A:G	F7L	0.722
X:52652899:T:G	K52T	0.721
X:52652919:T:A	K45N	0.721

dbSNP variants (sampled 300 via entrez): RS111730587 (X:52655664 A>AT,ATTTTAT,ATTTTATTTTAT,ATTTTATTTTATTTTAT), RS112111558 (X:52645439 G>A,C), RS112211534 (X:52649420 A>G), RS112382781 (X:52645464 G>T), RS112751012 (X:52644508 A>G,T), RS112961239 (X:52647974 T>C), RS113427843 (X:52649017 A>G), RS1156330277 (X:52647310 C>G), RS1156573993 (X:52647417 A>G,T), RS1156643653 (X:52646392 G>A,C), RS1157103519 (X:52651421 C>T), RS1157168018 (X:52652421 C>T), RS1157368726 (X:52650322 C>T), RS1157492422 (X:52644286 G>A), RS1157572526 (X:52656188 C>T)

Disease associations

OMIM: gene MIM:300542 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1

Clinical trials (associated diseases)

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