TEX12

Summary

TEX12 (testis expressed 12, HGNC:11734) is a protein-coding gene on chromosome 11q23.1, encoding Testis-expressed protein 12 (Q9BXU0). Component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase.

This gene is similar to a mouse gene that is expressed in the testis.

Source: NCBI Gene 56158 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 19 total
• MANE Select transcript: NM_031275

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11734
Approved symbol	TEX12
Name	testis expressed 12
Location	11q23.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000150783
Ensembl biotype	protein_coding
OMIM	605791
Entrez	56158

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000280358, ENST00000530752, ENST00000863453

RefSeq mRNA: 1 — MANE Select: NM_031275 NM_031275

CCDS: CCDS31679

Canonical transcript exons

ENST00000280358 — 5 exons

Exon	Start	End
ENSE00001409147	112167372	112167487
ENSE00001506867	112171772	112172556
ENSE00003508978	112169253	112169331
ENSE00003641208	112170419	112170530
ENSE00003651395	112170623	112170674

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 91.42.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0313 / max 31.1249, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116711	0.0158	4
116710	0.0155	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.42	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.59	gold quality
right testis	UBERON:0004534	82.19	gold quality
left testis	UBERON:0004533	81.47	gold quality
testis	UBERON:0000473	79.99	gold quality
buccal mucosa cell	CL:0002336	76.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	61.11	gold quality
monocyte	CL:0000576	60.44	gold quality
mononuclear cell	CL:0000842	60.34	gold quality
gastrocnemius	UBERON:0001388	60.23	gold quality
adult organism	UBERON:0007023	60.13	gold quality
muscle of leg	UBERON:0001383	59.97	gold quality
right coronary artery	UBERON:0001625	58.99	gold quality
leukocyte	CL:0000738	58.38	gold quality
muscle organ	UBERON:0001630	57.07	gold quality
popliteal artery	UBERON:0002250	55.76	gold quality
tibial artery	UBERON:0007610	55.74	gold quality
skin of leg	UBERON:0001511	54.76	gold quality
skin of abdomen	UBERON:0001416	54.59	gold quality
calcaneal tendon	UBERON:0003701	54.55	gold quality
aorta	UBERON:0000947	54.19	gold quality
smooth muscle tissue	UBERON:0001135	53.91	gold quality
descending thoracic aorta	UBERON:0002345	53.36	gold quality
lower esophagus mucosa	UBERON:0035834	53.34	gold quality
ectocervix	UBERON:0012249	53.12	gold quality
mucosa of stomach	UBERON:0001199	53.11	gold quality
zone of skin	UBERON:0000014	52.92	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	52.69	gold quality
thoracic aorta	UBERON:0001515	52.28	gold quality
ascending aorta	UBERON:0001496	52.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.78

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F6

miRNA regulators (miRDB)

40 targeting TEX12, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-3606-5P	99.31	69.67	1168
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-4528	99.18	69.77	1936

Literature-anchored findings (GeneRIF, showing 5)

• a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC. (PMID:22870393)
• This result suggests that regular expression of TEX11, TEX12, TEX14 and TEX15 is essential for the early stages of spermatogenesis. (PMID:29932616)
• Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12. (PMID:34373646)
• Centrosome dysfunction associated with somatic expression of the synaptonemal complex protein TEX12. (PMID:34880391)
• A Novel Frameshift Microdeletion of the TEX12 Gene Caused Infertility in Two Brothers with Nonobstructive Azoospermia. (PMID:37012491)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tex12	ENSMUSG00000032065
rattus_norvegicus	Tex12	ENSRNOG00000049470

Protein

Protein identifiers

Testis-expressed protein 12 — Q9BXU0 (reviewed: Q9BXU0)

All UniProt accessions (1): Q9BXU0

UniProt curated annotations — full annotation on UniProt →

Function. Component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element.

Subunit / interactions. Interacts with SYCE2.

Subcellular location. Chromosome.

Tissue specificity. Testis specific.

RefSeq proteins (1): NP_112565* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029193	TEX12	Family

Pfam: PF15219

UniProt features (5 total): compositionally biased region 2, chain 1, region of interest 1, helix 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
6HK9	X-RAY DIFFRACTION	1.45
6HK8	X-RAY DIFFRACTION	2.11
6R2F	X-RAY DIFFRACTION	2.29
6R17	X-RAY DIFFRACTION	2.42
6YQF	X-RAY DIFFRACTION	3.33

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXU0-F1	80.40	0.58

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-1221632	Meiotic synapsis
R-HSA-1474165	Reproduction
R-HSA-1500620	Meiosis
R-HSA-1640170	Cell Cycle

MSigDB gene sets: 90 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, REACTOME_MEIOTIC_SYNAPSIS, GOBP_SYNAPTONEMAL_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_FISSION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, GOBP_DNA_DAMAGE_RESPONSE, GOBP_CHROMOSOME_ORGANIZATION_INVOLVED_IN_MEIOTIC_CELL_CYCLE, GOBP_DNA_BIOSYNTHETIC_PROCESS, GOBP_DNA_SYNTHESIS_INVOLVED_IN_DNA_REPAIR, GOBP_HOMOLOGOUS_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP, WEBER_METHYLATED_ICP_IN_SPERM_DN, GOBP_HOMOLOGOUS_CHROMOSOME_PAIRING_AT_MEIOSIS

GO Biological Process (3): meiotic DNA repair synthesis (GO:0000711), synaptonemal complex assembly (GO:0007130), meiotic cell cycle (GO:0051321)

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

GO Cellular Component (3): central element (GO:0000801), chromosome (GO:0005694), synaptonemal complex (GO:0000795)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Meiosis	1
Reproduction	1
Cell Cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA synthesis involved in DNA repair	1
meiosis I cell cycle process	1
homologous chromosome pairing at meiosis	1
cellular component assembly	1
chromosome organization involved in meiotic cell cycle	1
synaptonemal complex organization	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
binding	1
synaptonemal complex	1
cellular anatomical structure	1
intracellular membraneless organelle	1
synaptonemal structure	1

Protein interactions and networks

STRING

486 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TEX12	SYCE2	Q6PIF2	997
TEX12	SYCE1	Q8N0S2	987
TEX12	SYCE3	A1L190	969
TEX12	SYCP1	Q15431	968
TEX12	SYCP3	Q8IZU3	922
TEX12	C14orf39	Q8N1H7	866
TEX12	SYCP2	Q9BX26	809
TEX12	HORMAD1	Q86X24	749
TEX12	HORMAD2	Q8N7B1	598
TEX12	SPO11	Q9Y5K1	594
TEX12	RAD21L1	Q9H4I0	593
TEX12	REC8	O95072	586
TEX12	STAG3	Q9UJ98	583
TEX12	SMC1B	Q8NDV3	575
TEX12	TEX15	Q9BXT5	558

IntAct

93 interactions, top by confidence:

A	B	Type	Score
SGF29	TEX12	psi-mi:“MI:0915”(physical association)	0.560
ZNF835	TEX12	psi-mi:“MI:0915”(physical association)	0.560
NUP54	TEX12	psi-mi:“MI:0915”(physical association)	0.560
INCA1	TEX12	psi-mi:“MI:0915”(physical association)	0.560
FAM161B	TEX12	psi-mi:“MI:0915”(physical association)	0.560
TEX12	FAM9C	psi-mi:“MI:0915”(physical association)	0.560
TEX12	LENG1	psi-mi:“MI:0915”(physical association)	0.560
TEX12	ZNF835	psi-mi:“MI:0915”(physical association)	0.560
FAM9C	TEX12	psi-mi:“MI:0915”(physical association)	0.560
LENG1	TEX12	psi-mi:“MI:0915”(physical association)	0.560
AP2B1	TEX12	psi-mi:“MI:0915”(physical association)	0.560
AIMP2	TEX12	psi-mi:“MI:0915”(physical association)	0.560
PPP1R13B	TEX12	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	TEX12	psi-mi:“MI:0915”(physical association)	0.560
CCNC	TEX12	psi-mi:“MI:0915”(physical association)	0.560
OIP5	TEX12	psi-mi:“MI:0915”(physical association)	0.560
MESD	TEX12	psi-mi:“MI:0915”(physical association)	0.560
SMARCE1	TEX12	psi-mi:“MI:0915”(physical association)	0.560
COX5B	TEX12	psi-mi:“MI:0915”(physical association)	0.560
SUOX	TEX12	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (20): TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), TEX12 (Two-hybrid), MSGN1 (Two-hybrid), FAM161B (Two-hybrid), SYCE2 (Two-hybrid)

ESM2 similar proteins: A0A1P8ARG1, A0A1S3X835, A6NKT7, B3LHE1, E7KNG0, E7NHN2, E7Q3U9, F4HVS6, F4HYG2, F4I131, F4IJK1, F4KEW8, O48767, O95816, P0DMS1, P21651, P46640, P48002, Q10006, Q12912, Q1T763, Q2T9U9, Q3UYG1, Q3ZBG5, Q56WM6, Q5XVI1, Q811D2, Q8LPQ1, Q8S8C6, Q91YN9, Q93ZY2, Q94CG5, Q94FL6, Q9BXU0, Q9C8Y4, Q9C9F5, Q9CR81, Q9FG14, Q9FX84, Q9LEZ4

Diamond homologs: Q9BXU0, Q9CR81

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
TEX12	“form complex”	Synaptonemal_complex	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

979 predictions. Top by Δscore:

Variant	Effect	Δscore
11:112167412:G:GT	donor_gain	1.0000
11:112170408:T:TA	acceptor_gain	1.0000
11:112170417:A:AG	acceptor_gain	1.0000
11:112170418:G:GA	acceptor_gain	1.0000
11:112170418:G:GG	acceptor_gain	1.0000
11:112170418:GT:G	acceptor_gain	1.0000
11:112171770:A:AG	acceptor_gain	1.0000
11:112171771:G:GG	acceptor_gain	1.0000
11:112171936:C:G	donor_gain	1.0000
11:112167415:G:GG	donor_gain	0.9900
11:112167483:G:GT	donor_gain	0.9900
11:112167484:A:T	donor_gain	0.9900
11:112167495:G:GT	donor_gain	0.9900
11:112170405:T:G	acceptor_gain	0.9900
11:112170413:T:A	acceptor_gain	0.9900
11:112170414:GTTA:G	acceptor_loss	0.9900
11:112170418:GTC:G	acceptor_gain	0.9900
11:112170418:GTCT:G	acceptor_gain	0.9900
11:112170418:GTCTC:G	acceptor_gain	0.9900
11:112170533:G:GT	donor_gain	0.9900
11:112171771:GT:G	acceptor_gain	0.9900
11:112171771:GTGA:G	acceptor_gain	0.9900
11:112171889:A:AG	donor_gain	0.9900
11:112171890:G:GG	donor_gain	0.9900
11:112171893:A:AG	donor_gain	0.9900
11:112171894:T:G	donor_gain	0.9900
11:112171913:A:G	donor_gain	0.9900
11:112167395:G:GT	donor_gain	0.9800
11:112167396:A:T	donor_gain	0.9800
11:112167483:G:T	donor_gain	0.9800

AlphaMissense

812 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:112171861:A:T	K106I	0.991
11:112171830:G:C	A96P	0.989
11:112171873:T:C	L110P	0.977
11:112171852:T:C	L103P	0.972
11:112171862:A:C	K106N	0.963
11:112171862:A:T	K106N	0.963
11:112171876:G:C	R111P	0.963
11:112171779:G:C	A79P	0.959
11:112171861:A:C	K106T	0.955
11:112170661:G:C	A72P	0.952
11:112171791:G:C	A83P	0.952
11:112171819:T:C	L92P	0.952
11:112171865:A:C	R107S	0.948
11:112171865:A:T	R107S	0.948
11:112171894:T:A	I117N	0.947
11:112171831:C:A	A96D	0.941
11:112171885:T:C	F114S	0.941
11:112171873:T:G	L110R	0.940
11:112171896:G:C	A118P	0.934
11:112171873:T:A	L110Q	0.932
11:112171906:T:C	L121S	0.932
11:112171782:G:C	A80P	0.923
11:112170671:T:C	L75S	0.917
11:112171894:T:G	I117S	0.907
11:112169316:G:C	R16S	0.905
11:112169316:G:T	R16S	0.905
11:112171789:A:T	D82V	0.904
11:112171843:A:T	E100V	0.897
11:112170668:T:C	L74P	0.894
11:112171852:T:A	L103Q	0.891

dbSNP variants (sampled 300 via entrez): RS1000638355 (11:112172350 AT>A,ATT), RS1000974740 (11:112172244 T>C), RS1000987659 (11:112172046 T>C), RS1001115507 (11:112165457 C>T), RS1001346612 (11:112166485 T>A), RS1001698495 (11:112166143 T>A), RS1002805417 (11:112171586 T>G), RS1002831237 (11:112171456 G>A,T), RS1003235889 (11:112169766 C>T), RS1003473356 (11:112170306 G>A), RS1003929188 (11:112171187 C>T), RS1004023983 (11:112170934 A>G), RS1004595689 (11:112166324 A>G), RS1005035655 (11:112165973 A>C), RS1005746839 (11:112171421 T>C)

Disease associations

OMIM: gene MIM:605791 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002255_1	Inflammatory biomarkers	2.000000e-32

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004812	interleukin-1 beta measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

3 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs187238	IL18, TEX12	3	2.50	1	interferons;ribavirin
rs1946518	IL18, TEX12	3	3.25	2	tacrolimus;interferons;ribavirin
rs5744247	IL18, TEX12	3	2.25	1	tacrolimus

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
fluorene-9-bisphenol	decreases expression	1
sodium arsenate	decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Folic Acid	decreases expression	1
Lead	affects methylation	1
Methotrexate	decreases expression	1
Progesterone	affects response to substance	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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