TEX28

Summary

TEX28 (testis expressed 28, HGNC:2563) is a protein-coding gene on chromosome Xq28, encoding Testis-specific protein TEX28 (O15482).

Predicted to be located in membrane. Predicted to be active in endomembrane system.

Source: NCBI Gene 1527 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001586

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2563
Approved symbol	TEX28
Name	testis expressed 28
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	fTEX
Ensembl gene	ENSG00000278057
Ensembl biotype	protein_coding
OMIM	300092
Entrez	1527

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000610938, ENST00000617213, ENST00000617225, ENST00000619903

RefSeq mRNA: 2 — MANE Select: NM_001586 NM_001205201, NM_001586

CCDS: CCDS14744

Canonical transcript exons

ENST00000617225 — 5 exons

Exon	Start	End
ENSE00003711901	154272391	154272526
ENSE00003731449	154287680	154288407
ENSE00003746610	154292106	154292205
ENSE00003751970	154271265	154271771
ENSE00003978288	154295030	154295124

Expression profiles

Bgee: expression breadth broad, 19 present calls, max score 89.51.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4151 / max 175.2569, expressed in 33 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
209878	0.4151	33

Top tissues by expression

122 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	89.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.76	gold quality
left testis	UBERON:0004533	73.07	gold quality
testis	UBERON:0000473	72.66	gold quality
right testis	UBERON:0004534	72.50	gold quality
granulocyte	CL:0000094	45.51	silver quality
blood	UBERON:0000178	37.63	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
bone marrow	UBERON:0002371	36.68	gold quality
skeletal muscle tissue	UBERON:0001134	36.56	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
sural nerve	UBERON:0015488	35.68	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle tissue	UBERON:0002385	33.40	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
liver	UBERON:0002107	28.33	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
tonsil	UBERON:0002372	27.05	gold quality
skin of leg	UBERON:0001511	26.84	gold quality
urinary bladder	UBERON:0001255	26.78	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
monocyte	CL:0000576	26.38	gold quality
zone of skin	UBERON:0000014	26.11	gold quality
gall bladder	UBERON:0002110	25.98	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-111727	no	845.22
E-ANND-3	no	0.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

11 targeting TEX28, 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-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-1249-5P	99.61	66.55	2049
HSA-MIR-6797-5P	99.61	66.55	2084
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-4456	97.50	64.88	1678

Literature-anchored findings (GeneRIF, showing 2)

• proposed a structure of the second gene of 3-gene arrays, Green-pTEX-Green-pTEX-Green-fTEX and Red-pTEX-Red-pTEX-Red-fTEX, in color-vision-deficient subjects (PMID:15378397)
• TEX28 gene CNVs (copy number variations) appear to be associated with the MYP1 X-linked myopia phenotypes. (PMID:19098318)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tex28	ENSMUSG00000062564
rattus_norvegicus	Tex28	ENSRNOG00000051438
drosophila_melanogaster	Dmtn	FBGN0037443
caenorhabditis_elegans		WBGENE00015800

Paralogs (3): TMCC3 (ENSG00000057704), TMCC2 (ENSG00000133069), TMCC1 (ENSG00000172765)

Protein

Protein identifiers

Testis-specific protein TEX28 — O15482 (reviewed: O15482)

All UniProt accessions (1): O15482

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Testis specific.

Similarity. Belongs to the TEX28 family.

RefSeq proteins (2): NP_001192130, NP_001577* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017387	Testis-specific_TEX28	Family
IPR019394	TEX28/TMCC	Family

Pfam: PF10267

UniProt features (8 total): region of interest 2, coiled-coil region 2, compositionally biased region 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O15482-F1	75.02	0.45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): MODULE_379, MODULE_242, MODULE_104, CAMPS_COLON_CANCER_COPY_NUMBER_DN, MODULE_13, MODULE_181, MORF_DDX11, chrXq28, MODULE_41, MIR876_3P, GSE10147_IL3_AND_HIVP17_VS_IL3_AND_CPG_STIM_PDC_DN, ZAK_PBMC_MRKAD5_HIV_1_GAG_POL_NEF_AGE_20_50YO_CORRELATED_WITH_CD8_T_CELL_RESPONSE_3DY_NEGATIVE, NAKAYA_MYELOID_DENDRITIC_CELL_FLUARIX_FLUVIRIN_AGE_18_50YO_7DY_DN, GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN, GSE3982_MAC_VS_CENT_MEMORY_CD4_TCELL_DN

GO Biological Process (0):

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

GO Cellular Component (2): endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
binding	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TEX28	TKTL1	P51854	921
TEX28	OPN1LW	P04000	897
TEX28	TEX13A	Q9BXU3	587
TEX28	HAUS7	Q99871	510
TEX28	OPN1MW2	P0DN77	507
TEX28	TEX13C	A0A0J9YWL9	439
TEX28	PNCK	Q6P2M8	401
TEX28	ZNF275	Q9NSD4	400
TEX28	RENBP	P51606	397
TEX28	NAA10	P41227	372
TEX28	SPRY3	O43610	367
TEX28	TEX13D	A0A0J9YY54	363
TEX28	TEX36	Q5VZQ5	359
TEX28	DYNAP	Q8N1N2	349
TEX28	CSAG1	Q6PB30	348

IntAct

21 interactions, top by confidence:

A	B	Type	Score
TEX28	TMCC3	psi-mi:“MI:0915”(physical association)	0.800
TEX28	TMCC2	psi-mi:“MI:0914”(association)	0.640
TEX28	CDR2	psi-mi:“MI:0915”(physical association)	0.560
TEX28	KRT31	psi-mi:“MI:0915”(physical association)	0.560
TEX28	KRT27	psi-mi:“MI:0915”(physical association)	0.560
TEX28	ZNF655	psi-mi:“MI:0915”(physical association)	0.560
TEX28	EPS8	psi-mi:“MI:0915”(physical association)	0.370
TEX28	NBAS	psi-mi:“MI:0914”(association)	0.350
TEX28	PRAF2	psi-mi:“MI:0914”(association)	0.350
TEX28	CDR2	psi-mi:“MI:0915”(physical association)	0.000
TEX28	KRT27	psi-mi:“MI:0915”(physical association)	0.000
TEX28	KRT31	psi-mi:“MI:0915”(physical association)	0.000
TMCC3	TEX28	psi-mi:“MI:0915”(physical association)	0.000
TEX28	ZNF655	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (56): EPS8 (Two-hybrid), TMCC2 (Affinity Capture-MS), TMCC1 (Affinity Capture-MS), TMCC3 (Affinity Capture-MS), TRPM7 (Affinity Capture-MS), KIF14 (Affinity Capture-MS), KIAA0100 (Affinity Capture-MS), TRIM13 (Affinity Capture-MS), SELT (Affinity Capture-MS), SARAF (Affinity Capture-MS), PDE3B (Affinity Capture-MS), BNIP1 (Affinity Capture-MS), SMPD2 (Affinity Capture-MS), UPK3BL (Affinity Capture-MS), TMEM201 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WVF3, A0A087WXS9, A0A087X179, A0A087X1G2, A6NDS4, A6NER0, A6QPT6, B9A6J9, M3WHG5, O14771, O15482, O15553, O19110, O76081, P0C7X1, P0C7X3, P0C7X4, P35125, P48778, P48967, P79209, Q13670, Q15697, Q2TBC4, Q3T191, Q3UZD7, Q4R2Z8, Q5DRQ5, Q5SSQ6, Q5XFX8, Q69ZB3, Q6DHY5, Q6IPX1, Q6ZMN8, Q8BLR5, Q8BWA8, Q8IYF1, Q8IZP1, Q8JZW5, Q8N7G0

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	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

21 predictions. Top by Δscore:

Variant	Effect	Δscore
X:154295821:C:G	donor_gain	0.9800
X:154295828:G:GG	donor_gain	0.9400
X:154295819:GAC:G	donor_gain	0.9300
X:154295825:GGA:G	donor_gain	0.9200
X:154295826:GAG:G	donor_gain	0.9200
X:154295827:A:AG	donor_gain	0.9200
X:154295824:AGG:A	donor_gain	0.9100
X:154295822:G:GG	donor_gain	0.7800
X:154295826:GA:G	donor_gain	0.7400
X:154295817:GAGAC:G	donor_gain	0.5000
X:154295819:G:GT	donor_gain	0.4700
X:154295823:TAG:T	donor_gain	0.4400
X:154295826:G:GT	donor_gain	0.4300
X:154295727:G:GT	donor_gain	0.4000
X:154295831:G:A	donor_gain	0.3900
X:154295827:A:T	donor_gain	0.3500
X:154295825:G:A	donor_gain	0.3200
X:154295825:G:GT	donor_gain	0.3100
X:154295830:G:A	donor_gain	0.2200
X:154295834:C:A	donor_gain	0.2200
X:154295723:G:GA	donor_gain	0.2000

AlphaMissense

2672 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:154288135:A:C	F95L	0.937
X:154288135:A:T	F95L	0.937
X:154288137:A:G	F95L	0.937
X:154272461:A:G	L269P	0.827
X:154288256:A:G	I55T	0.823
X:154287764:A:G	L219P	0.810
X:154287719:A:G	L234P	0.787
X:154271754:G:C	F298L	0.771
X:154271754:G:T	F298L	0.771
X:154271756:A:G	F298L	0.771
X:154288241:T:A	E60V	0.764
X:154288082:A:G	L113P	0.761
X:154288225:C:A	E65D	0.757
X:154288225:C:G	E65D	0.757
X:154272457:T:A	K270N	0.742
X:154272457:T:G	K270N	0.742
X:154288235:A:G	L62P	0.740
X:154272400:C:A	K289N	0.737
X:154272400:C:G	K289N	0.737
X:154272458:T:A	K270I	0.737
X:154288238:T:G	Q61P	0.737
X:154288247:A:G	L58P	0.722
X:154287786:C:G	A212P	0.720
X:154288061:A:G	L120P	0.720
X:154287743:A:G	L226P	0.708
X:154287794:A:G	L209P	0.707
X:154288245:A:G	S59P	0.704
X:154288240:C:A	E60D	0.699
X:154288240:C:G	E60D	0.699
X:154287707:A:G	L238P	0.696

dbSNP variants (sampled 300 via entrez): RS1002425912 (X:154296798 T>C), RS1002915230 (X:154295264 G>T), RS1004768784 (X:154296215 G>A,T), RS1008905043 (X:154296454 G>A,T), RS1009616761 (X:154297002 G>C), RS1010080738 (X:154296767 C>T), RS1012974974 (X:154295256 C>A,T), RS1013315141 (X:154295040 G>C), RS1013857106 (X:154297120 C>G,T), RS1015745159 (X:154297135 G>A), RS1016401533 (X:154295342 G>A), RS1016928734 (X:154295625 T>A,G), RS1021531145 (X:154295776 C>T), RS1022272330 (X:154296780 C>T), RS1022941503 (X:154295065 T>C)

Disease associations

OMIM: gene MIM:300092 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): X-linked Emery-Dreifuss muscular dystrophy (MONDO:0010680)

Orphanet (2): Emery-Dreifuss muscular dystrophy (Orphanet:261), X-linked Emery-Dreifuss muscular dystrophy (Orphanet:98863)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D000083143	X-Linked Emery-Dreifuss Muscular Dystrophy	C05.651.534.500.350.500; C10.668.491.175.500.350.500; C16.320.322.625.500; C16.320.577.350.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	increases phosphorylation	1
Resveratrol	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03058185	Not specified	RECRUITING	Observatoire Des Patients Atteints de Laminopathies et Emerinopathies (Observatory for PAtients With Laminopathies and Emerinopathies)