TEX13A

Summary

TEX13A (testis expressed 13A, HGNC:11735) is a protein-coding gene on chromosome Xq22.3, encoding Testis-expressed protein 13A (Q9BXU3). Binds to ssRNA containing the consensus sequence 5’-AGGUAA-3'.

This gene is similar to a mouse gene that is expressed in the testis. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 56157 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total — 1 pathogenic
• Druggable target: yes
• MANE Select transcript: NM_031274

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11735
Approved symbol	TEX13A
Name	testis expressed 13A
Location	Xq22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000268629
Ensembl biotype	protein_coding
OMIM	300312
Entrez	56157

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000600991, ENST00000609007

RefSeq mRNA: 2 — MANE Select: NM_031274 NM_001291277, NM_031274

CCDS: CCDS76005

Canonical transcript exons

ENST00000600991 — 3 exons

Exon	Start	End
ENSE00002993733	105218929	105219758
ENSE00003156649	105219963	105220429
ENSE00003208722	105220595	105220694

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 81.73.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	81.73	silver quality
male germ cell	CL:0000015	79.73	silver quality
parotid gland	UBERON:0001831	74.06	gold quality
left testis	UBERON:0004533	73.98	gold quality
right testis	UBERON:0004534	72.81	gold quality
testis	UBERON:0000473	71.78	gold quality
heart right ventricle	UBERON:0002080	67.90	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	67.90	gold quality
nasal cavity epithelium	UBERON:0005384	66.55	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	65.91	gold quality
vastus lateralis	UBERON:0001379	62.04	gold quality
esophagus squamous epithelium	UBERON:0006920	61.81	gold quality
quadriceps femoris	UBERON:0001377	61.27	gold quality
myocardium	UBERON:0002349	61.20	gold quality
secondary oocyte	CL:0000655	61.16	gold quality
biceps brachii	UBERON:0001507	60.62	gold quality
epithelium of esophagus	UBERON:0001976	60.42	gold quality
vena cava	UBERON:0004087	60.09	gold quality
medial globus pallidus	UBERON:0002477	59.95	gold quality
oral cavity	UBERON:0000167	59.53	gold quality
superficial temporal artery	UBERON:0001614	59.48	gold quality
globus pallidus	UBERON:0001875	58.99	gold quality
upper arm skin	UBERON:0004263	58.58	gold quality
cerebellar vermis	UBERON:0004720	58.54	gold quality
adult organism	UBERON:0007023	58.18	gold quality
jejunal mucosa	UBERON:0000399	57.98	gold quality
pancreatic ductal cell	CL:0002079	57.87	silver quality
tibia	UBERON:0000979	57.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	57.00	gold quality
deltoid	UBERON:0001476	56.92	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.15

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Tex13a was identified as a spermatagonia-specific gene in mouse. (PMID:11279525)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG14718	FBGN0037939

Paralogs (3): TEX13B (ENSG00000170925), TEX13D (ENSG00000282419), TEX13C (ENSG00000282815)

Protein

Protein identifiers

Testis-expressed protein 13A — Q9BXU3 (reviewed: Q9BXU3)

All UniProt accessions (1): Q9BXU3

UniProt curated annotations — full annotation on UniProt →

Function. Binds to ssRNA containing the consensus sequence 5’-AGGUAA-3’. Plays a role in transcriptional repression. Required for rapid sperm motility and timely degradation of mRNA via its interaction with CNOT1.

Subunit / interactions. Interacts with CNOT1; the interaction may inhibit CNOT1 binding to mRNA and subsequently CNOT1-mediated mRNA degradation.

Tissue specificity. Testis specific.

Similarity. Belongs to the TEX13 family.

RefSeq proteins (2): NP_001278206, NP_112564* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001876	Znf_RanBP2	Domain
IPR028193	TEX13A-D_N	Domain
IPR036443	Znf_RanBP2_sf	Homologous_superfamily
IPR049534	TEX13A/C/D_Znf	Domain
IPR054602

Pfam: PF15186, PF20864, PF22835

UniProt features (9 total): binding site 4, region of interest 2, chain 1, zinc finger region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXU3-F1	64.36	0.32

Functional residue map

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

Ligand- & substrate-binding residues (4): 382; 385; 396; 399

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_UP, FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP, GOMF_MRNA_BINDING, chrXq22, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ALK_DN.V1_DN, IL2_UP.V1_UP, IL21_UP.V1_UP, KRAS.LUNG_UP.V1_UP, GSE11864_CSF1_VS_CSF1_IFNG_PAM3CYS_IN_MAC_UP, GSE19825_NAIVE_VS_DAY3_EFF_CD8_TCELL_UP, GSE22886_NAIVE_CD8_TCELL_VS_NEUTROPHIL_DN, GSE3982_CTRL_VS_PMA_STIM_EOSINOPHIL_DN, GSE3982_EOSINOPHIL_VS_BASOPHIL_UP, GSE7460_TCONV_VS_TREG_LN_UP

GO Biological Process (0):

GO Molecular Function (5): mRNA binding (GO:0003729), zinc ion binding (GO:0008270), RNA binding (GO:0003723), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

894 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TEX13A	TEX28	O15482	587
TEX13A	ZNF711	Q9Y462	488
TEX13A	AKAP4	Q5JQC9	478
TEX13A	ZFX	P17010	469
TEX13A	DIAPH2	O60879	461
TEX13A	AFF2	P51816	460
TEX13A	PCYT1B	Q9Y5K3	426
TEX13A	CUL4B	Q13620	426
TEX13A	FNDC8	Q8TC99	417
TEX13A	HORMAD1	Q86X24	414
TEX13A	SCML2	Q9UQR0	411
TEX13A	TAF7L	Q5H9L4	409
TEX13A	TEX22	C9J3V5	396
TEX13A	HORMAD2	Q8N7B1	395
TEX13A	RLIM	Q9NVW2	394

IntAct

22 interactions, top by confidence:

A	B	Type	Score
TEX13A	TBC1D10A	psi-mi:“MI:0915”(physical association)	0.720
TBC1D10A	TEX13A	psi-mi:“MI:0915”(physical association)	0.720
ATP5PO	TEX13A	psi-mi:“MI:0915”(physical association)	0.560
TXN	TEX13A	psi-mi:“MI:0915”(physical association)	0.560
TTC23	TEX13A	psi-mi:“MI:0915”(physical association)	0.560
MYO15B	TEX13A	psi-mi:“MI:0915”(physical association)	0.560
TEX13A	CNOT1	psi-mi:“MI:0914”(association)	0.350
TBC1D10A	TEX13A	psi-mi:“MI:0915”(physical association)	0.000
ATP5PO	TEX13A	psi-mi:“MI:0915”(physical association)	0.000
MYO15B	TEX13A	psi-mi:“MI:0915”(physical association)	0.000
TXN	TEX13A	psi-mi:“MI:0915”(physical association)	0.000
TTC23	TEX13A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (43): TBC1D10A (Two-hybrid), CNOT6 (Affinity Capture-MS), CNOT6L (Affinity Capture-MS), CNOT8 (Affinity Capture-MS), RQCD1 (Affinity Capture-MS), CNOT11 (Affinity Capture-MS), CNOT1 (Affinity Capture-MS), CNOT7 (Affinity Capture-MS), CNOT10 (Affinity Capture-MS), SETD3 (Affinity Capture-MS), BTG3 (Affinity Capture-MS), SMARCD2 (Affinity Capture-MS), ASPM (Affinity Capture-MS), CNOT3 (Affinity Capture-MS), RNF20 (Affinity Capture-MS)

ESM2 similar proteins: A1YEW3, A1YG31, A2T715, A2T7M0, A6NEV1, A6NGD5, A6NJL1, A6QPT6, A8MXV6, A8MZF0, A8WFF7, O08664, P03327, P06936, P0C6A0, P0DPQ3, P54257, P57086, P86478, P86479, P86480, P86481, P86496, Q13487, Q32PG5, Q505G4, Q5R7P6, Q68FX5, Q6J1H4, Q6NZN1, Q6ZMS7, Q6ZRT6, Q76NI1, Q7L3V2, Q7TPK6, Q7YR42, Q7Z6I6, Q80UE6, Q8IY33, Q8K2W9

Diamond homologs: A0A0J9YWL9, A0A0J9YY54, A2AFS9, D3YU32, Q9BXU2, Q9BXU3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1526834	GRCh37/hg19 Xq22.1-24(chrX:101982475-116885339)	Pathogenic

SpliceAI

414 predictions. Top by Δscore:

Variant	Effect	Δscore
X:105219958:CTCA:C	donor_loss	1.0000
X:105219960:CACC:C	donor_loss	1.0000
X:105219962:C:CT	donor_loss	1.0000
X:105219959:TCA:T	donor_gain	0.9900
X:105219960:CAC:C	donor_gain	0.9900
X:105219961:A:AC	donor_gain	0.9900
X:105219962:C:CC	donor_gain	0.9900
X:105219957:ACT:A	donor_gain	0.9800
X:105219958:CTC:C	donor_gain	0.9800
X:105219961:ACCT:A	donor_gain	0.9800
X:105219962:C:G	donor_gain	0.9700
X:105220590:CTCAC:C	donor_loss	0.9700
X:105220592:CAC:C	donor_loss	0.9700
X:105220593:A:C	donor_loss	0.9700
X:105220594:CCTCT:C	donor_loss	0.9700
X:105220594:CCT:C	donor_gain	0.9600
X:105219956:AACT:A	donor_gain	0.9300
X:105219961:AC:A	donor_gain	0.9300
X:105219962:CC:C	donor_gain	0.9300
X:105219962:CCTT:C	donor_gain	0.9300
X:105220207:TTG:T	donor_gain	0.9000
X:105219755:GCTCC:G	acceptor_loss	0.8900
X:105219757:TCCTG:T	acceptor_loss	0.8900
X:105219758:CCT:C	acceptor_loss	0.8900
X:105219759:C:A	acceptor_loss	0.8900
X:105219760:T:G	acceptor_loss	0.8900
X:105220270:C:CT	acceptor_gain	0.8900
X:105220429:CCTG:C	acceptor_gain	0.8900
X:105219756:CTC:C	acceptor_gain	0.8700
X:105220217:TGGG:T	donor_gain	0.8600

AlphaMissense

2648 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:105219024:A:C	F390L	0.993
X:105219024:A:T	F390L	0.993
X:105219026:A:G	F390L	0.993
X:105220296:G:C	F34L	0.991
X:105220296:G:T	F34L	0.991
X:105220298:A:G	F34L	0.991
X:105219040:C:G	C385S	0.990
X:105219041:A:T	C385S	0.990
X:105219054:C:A	W380C	0.990
X:105219054:C:G	W380C	0.990
X:105220362:G:C	F12L	0.986
X:105220362:G:T	F12L	0.986
X:105220364:A:G	F12L	0.986
X:105220269:C:A	W43C	0.983
X:105220269:C:G	W43C	0.983
X:105220363:A:G	F12S	0.983
X:105220271:A:G	W43R	0.982
X:105220271:A:T	W43R	0.982
X:105220297:A:G	F34S	0.982
X:105219003:G:C	F397L	0.981
X:105219003:G:T	F397L	0.981
X:105219005:A:G	F397L	0.981
X:105220193:A:G	W69R	0.981
X:105220193:A:T	W69R	0.981
X:105219050:A:G	C382R	0.980
X:105220185:G:C	S71R	0.978
X:105220185:G:T	S71R	0.978
X:105220187:T:G	S71R	0.978
X:105219006:G:C	C396W	0.977
X:105219007:C:G	C396S	0.977

dbSNP variants (sampled 300 via entrez): RS1000334651 (X:105220649 C>G,T), RS1000873786 (X:105220937 C>A,T), RS1002776064 (X:105218533 G>A,C), RS1003929141 (X:105221654 C>T), RS1003946423 (X:105222090 G>A), RS1006400228 (X:105218517 G>A), RS1010177852 (X:105218892 A>C,G), RS1013522766 (X:105222253 A>G,T), RS1014496150 (X:105220602 G>A), RS1015245151 (X:105221668 A>C), RS1015690787 (X:105221280 T>C), RS1016651049 (X:105219863 C>A,T), RS1018107717 (X:105219188 A>C,T), RS1020450618 (X:105220333 T>A), RS1020587782 (X:105220630 C>T)

Disease associations

OMIM: gene MIM:300312 | 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: yes

ChEMBL targets (1): CHEMBL6066450 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.10	Kd	786.2	nM	CHEMBL5653589
6.10	ED50	786.2	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149573: Binding affinity to human TEX13A incubated for 45 mins by Kinobead based pull down assay	kd	0.7862	uM

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, decreases expression	1
Formaldehyde	increases expression	1
Valproic Acid	increases methylation	1
Particulate Matter	increases abundance, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652615	Binding	Binding affinity to human TEX13A incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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