TSBP1

Summary

TSBP1 (testis expressed basic protein 1, HGNC:13922) is a protein-coding gene on chromosome 6p21.32, encoding Testis-expressed basic protein 1 (Q5SRN2).

Located in nucleus.

Source: NCBI Gene 10665 — RefSeq curated summary.

At a glance

• GWAS associations: 137
• Clinical variants (ClinVar): 6 total
• MANE Select transcript: NM_001286474

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13922
Approved symbol	TSBP1
Name	testis expressed basic protein 1
Location	6p21.32
Locus type	gene with protein product
Status	Approved
Aliases	TSBP
Ensembl gene	ENSG00000204296
Ensembl biotype	protein_coding
OMIM	618151
Entrez	10665

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000375015, ENST00000442822, ENST00000447241, ENST00000527965, ENST00000532023, ENST00000533191, ENST00000534588, ENST00000698834

RefSeq mRNA: 3 — MANE Select: NM_001286474 NM_001286474, NM_001286475, NM_006781

CCDS: CCDS34422, CCDS69082, CCDS75430

Canonical transcript exons

ENST00000413045 — 0 exons

Expression profiles

Bgee: expression breadth broad, 58 present calls, max score 89.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0437 / max 33.8314, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
72945	0.0244	3
72946	0.0134	3
72944	0.0059	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	89.77	gold quality
testis	UBERON:0000473	89.33	gold quality
right testis	UBERON:0004534	88.88	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.10	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.51	gold quality
sural nerve	UBERON:0015488	55.74	gold quality
lymph node	UBERON:0000029	52.50	gold quality
bone marrow cell	CL:0002092	47.96	gold quality
colonic epithelium	UBERON:0000397	46.68	gold quality
calcaneal tendon	UBERON:0003701	46.04	silver quality
adrenal tissue	UBERON:0018303	45.37	gold quality
tonsil	UBERON:0002372	44.36	silver quality
uterine cervix	UBERON:0000002	42.99	silver quality
right ovary	UBERON:0002118	42.45	silver quality
ventricular zone	UBERON:0003053	42.31	gold quality
ovary	UBERON:0000992	41.35	gold quality
cortical plate	UBERON:0005343	41.27	gold quality
endometrium	UBERON:0001295	40.74	gold quality
left ovary	UBERON:0002119	39.71	gold quality
endocervix	UBERON:0000458	39.43	gold quality
ganglionic eminence	UBERON:0004023	39.03	gold quality
bone marrow	UBERON:0002371	38.91	gold quality
body of uterus	UBERON:0009853	38.12	silver quality
metanephros cortex	UBERON:0010533	35.71	silver quality
apex of heart	UBERON:0002098	35.45	gold quality
ectocervix	UBERON:0012249	35.24	silver quality
tibial nerve	UBERON:0001323	35.13	gold quality
vermiform appendix	UBERON:0001154	35.12	gold quality
granulocyte	CL:0000094	34.99	gold quality
duodenum	UBERON:0002114	34.79	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting TSBP1, 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-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-516B-5P	99.56	66.33	1495
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-6506-5P	99.04	65.66	1386
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-619-5P	98.57	64.97	1988
HSA-MIR-3689A-5P	98.35	70.12	1049
HSA-MIR-3689B-5P	98.35	70.12	1049
HSA-MIR-3689E	98.35	70.12	1049
HSA-MIR-3689F	98.35	70.08	1052
HSA-MIR-5087	98.01	69.09	965
HSA-MIR-4468	98.01	66.85	1187
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-15B-3P	97.85	66.68	974
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-6500-3P	97.42	67.20	867
HSA-MIR-2278	97.30	66.19	1130
HSA-MIR-4474-3P	96.97	65.87	870

Literature-anchored findings (GeneRIF, showing 4)

• Our findings suggest that CpG-single nucleotide polymorphisms at the C6orf10/LOC101929163 locus might modify age of onset in C9orf72 carriers belonging to the entire amyotrophic lateral sclerosis-frontotemporal dementia spectrum by controlling DNA methylation and gene expression (PMID:30252044)
• Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo. (PMID:33022050)
• Multilocus evaluation of genetic predictors of multiple sclerosis. (PMID:34656742)
• Impact of missense TSBP1 variants on the susceptibility to coronary heart disease. (PMID:38042215)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tsbp1	ENSMUSG00000057246
rattus_norvegicus	Tsbp1	ENSRNOG00000039398

Protein

Protein identifiers

Testis-expressed basic protein 1 — Q5SRN2 (reviewed: Q5SRN2)

Alternative names: Uncharacterized protein C6orf10

All UniProt accessions (7): A0A1U9X7D1, A0A8V8TNR9, C9J9T8, E9PLW3, E9PNQ4, E9PQ85, Q5SRN2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5SRN2-1	1	yes
Q5SRN2-2	2
Q5SRN2-3	3

RefSeq proteins (3): NP_001273403, NP_001273404, NP_006772 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038754	TSBP1	Family

UniProt features (28 total): sequence variant 14, compositionally biased region 5, splice variant 4, transmembrane region 2, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SRN2-F1	45.58	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, KRAS.600.LUNG.BREAST_UP.V1_DN, KRAS.BREAST_UP.V1_DN, KRAS.LUNG.BREAST_UP.V1_DN, ZNF146_TARGET_GENES, MIR4505, MIR5787, MIR5681A, FAN_EMBRYONIC_CTX_EX_4_EXCITATORY_NEURON, TTCYRGAA_UNKNOWN, DESCARTES_FETAL_MUSCLE_SCHWANN_CELLS, FOURATI_BLOOD_TWINRIX_AGE_25_83YO_RESPONDERS_VS_POOR_RESPONDERS_0DY_DN, GSE24081_CONTROLLER_VS_PROGRESSOR_HIV_SPECIFIC_CD8_TCELL_DN, GSE3982_MAC_VS_CENT_MEMORY_CD4_TCELL_DN, GSE3982_BCELL_VS_CENT_MEMORY_CD4_TCELL_DN

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

354 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TSBP1	BTNL2	Q9UIR0	697
TSBP1	TTC32	Q5I0X7	591
TSBP1	MICB	P79525	539
TSBP1	COL11A2	P13942	531
TSBP1	NOTCH4	Q99466	527
TSBP1	HLA-DRA	P01903	507
TSBP1	HLA-DRB1	P01911	505
TSBP1	HLA-DQB1	P01917	479
TSBP1	PSORS1C1	Q9UIG5	471
TSBP1	E7ENX8	E7ENX8	448
TSBP1	Q5Y7H0	Q5Y7H0	446
TSBP1	TNF	P01375	432
TSBP1	BRD2	P25440	429
TSBP1	RNF5	Q99942	417
TSBP1	TNXB	P22105	417

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ARHGAP18	CLTB	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): C6orf10 (Biochemical Activity), C6orf10 (Affinity Capture-MS), C6orf10 (Cross-Linking-MS (XL-MS)), C6orf10 (Cross-Linking-MS (XL-MS)), C6orf10 (Affinity Capture-MS), C6orf10 (Proximity Label-MS)

ESM2 similar proteins: A0A060XQP6, A0A1S4FQ37, A2VD23, A3KQQ9, A7E371, B3A0Q3, B3EWZ0, B3EWZ1, B3EWZ4, B7W112, D1FQ14, E9Q9K5, G5EC21, O01949, O16883, O43493, O46203, O55188, O84462, P08721, P10451, P10923, P13665, P14287, P19814, P23498, P31096, P31097, P31098, P31936, P35662, P35663, P98193, Q13316, Q14093, Q28139, Q5MIT9, Q5SRN2, Q5UQ32, Q62313

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2509 predictions. Top by Δscore:

Variant	Effect	Δscore
6:32335910:A:AC	donor_gain	1.0000
6:32335911:C:CC	donor_gain	1.0000
6:32337187:T:TA	donor_gain	1.0000
6:32300701:C:CC	acceptor_gain	0.9900
6:32302607:A:AC	donor_gain	0.9900
6:32302608:C:CC	donor_gain	0.9900
6:32302628:TCCTG:T	acceptor_loss	0.9900
6:32302629:CCTGA:C	acceptor_loss	0.9900
6:32302630:CTG:C	acceptor_loss	0.9900
6:32331958:TAA:T	donor_gain	0.9900
6:32331959:AAA:A	donor_gain	0.9900
6:32331960:A:C	donor_gain	0.9900
6:32335933:C:CC	acceptor_gain	0.9900
6:32355648:C:CT	donor_gain	0.9900
6:32300678:A:AC	donor_gain	0.9800
6:32300679:C:CC	donor_gain	0.9800
6:32302608:CTA:C	donor_gain	0.9800
6:32302631:T:A	acceptor_loss	0.9800
6:32331959:A:AC	donor_gain	0.9800
6:32335907:CT:C	donor_loss	0.9800
6:32335908:TT:T	donor_loss	0.9800
6:32335911:C:CT	donor_loss	0.9800
6:32355647:A:AC	donor_gain	0.9800
6:32369896:CCA:C	donor_gain	0.9800
6:32302608:CTAG:C	donor_gain	0.9700
6:32335933:CTGTG:C	acceptor_loss	0.9700
6:32335934:T:G	acceptor_loss	0.9700
6:32335935:G:C	acceptor_gain	0.9700
6:32335935:G:GC	acceptor_gain	0.9700
6:32355678:A:C	acceptor_gain	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000007662 (6:32351023 T>A,C), RS1000067287 (6:32321111 G>GT), RS1000078036 (6:32371552 A>G), RS1000129903 (6:32371298 C>T), RS1000132775 (6:32334966 G>A), RS1000138973 (6:32322811 C>T), RS1000144699 (6:32350561 G>T), RS1000184669 (6:32332383 A>G), RS1000329283 (6:32342630 A>G), RS1000381928 (6:32342351 C>T), RS1000420138 (6:32320830 C>T), RS1000440099 (6:32335267 A>G), RS1000492815 (6:32309701 G>T), RS1000602977 (6:32297980 T>A), RS1000659344 (6:32348647 C>G)

Disease associations

OMIM: gene MIM:618151 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

137 associations (top):

Study	Trait	p-value
GCST000180_4	Bone mineral density (spine)	1.000000e-07
GCST000408_6	Primary biliary cholangitis	1.000000e-10
GCST000408_7	Primary biliary cholangitis	7.000000e-10
GCST000624_3	Ulcerative colitis	9.000000e-23
GCST000981_1	Vitiligo	8.000000e-11
GCST000984_17	Idiopathic membranous nephropathy	2.000000e-40
GCST000984_4	Idiopathic membranous nephropathy	5.000000e-71
GCST000996_22	Systemic lupus erythematosus	3.000000e-06
GCST001183_6	Asthma	3.000000e-15
GCST001459_1	Multiple sclerosis	7.000000e-16
GCST001525_5	Visceral fat	3.000000e-06
GCST001574_8	Activated partial thromboplastin time	7.000000e-07
GCST001587_6	Coronary heart disease	3.000000e-15
GCST001709_7	Atopic dermatitis	5.000000e-19
GCST001762_369	Obesity-related traits	2.000000e-06
GCST001815_1	Hepatitis C induced liver cirrhosis	9.000000e-11
GCST001942_21	Prostate cancer	5.000000e-09
GCST002097_4	Coronary artery calcification	3.000000e-06
GCST002217_4	Sjögren’s syndrome	9.000000e-37
GCST002297_1	Hepatitis B vaccine response	3.000000e-19
GCST002300_1	Rheumatoid arthritis	3.000000e-12
GCST002479_16	Lupus nephritis in systemic lupus erythematosus	2.000000e-06
GCST002737_3	Atopic dermatitis	4.000000e-08
GCST003450_2	Clozapine-induced agranulocytosis/granulocytopenia in treatment-resistant schizophrenia	3.000000e-09
GCST003773_15	Loneliness (multivariate analysis)	2.000000e-06
GCST004122_3	Fibrinogen levels	9.000000e-09
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_1	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_10	Autism spectrum disorder or schizophrenia	2.000000e-13

EFO canonical traits (19, from GWAS)

EFO ID	Trait name
EFO:0004267	biliary liver cirrhosis
EFO:0003939	energy intake
EFO:0004723	coronary artery calcification
EFO:0004645	response to vaccine
EFO:0007865	loneliness measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008002	physical activity measurement
EFO:0007986	reticulocyte count
EFO:0004587	lymphocyte count
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0008378	mosquito bite reaction size measurement
EFO:0009180	rosacea severity measurement
EFO:0004808	L lactate dehydrogenase measurement
EFO:0006336	diastolic blood pressure
EFO:0004509	hemoglobin measurement
EFO:0009819	comparative body size at age 10, self-reported
EFO:0004918	age at diagnosis
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference

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
Silicon Dioxide	decreases expression	2
bisphenol A	affects methylation	1
butyraldehyde	decreases expression	1
aflatoxin B2	increases methylation	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases expression	1
Catechin	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1

Clinical trials (associated diseases)

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