TCEAL2

Summary

TCEAL2 (transcription elongation factor A like 2, HGNC:29818) is a protein-coding gene on chromosome Xq22.1, encoding Transcription elongation factor A protein-like 2 (Q9H3H9). May be involved in transcriptional regulation.

This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome.

Source: NCBI Gene 140597 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_080390

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29818
Approved symbol	TCEAL2
Name	transcription elongation factor A like 2
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	my048, MY0876G05, WEX1
Ensembl gene	ENSG00000184905
Ensembl biotype	protein_coding
OMIM	301152
Entrez	140597

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000329035, ENST00000372780, ENST00000476749, ENST00000651085, ENST00000902218, ENST00000936754, ENST00000944951, ENST00000944952

RefSeq mRNA: 1 — MANE Select: NM_080390 NM_080390

CCDS: CCDS14496

Canonical transcript exons

ENST00000372780 — 3 exons

Exon	Start	End
ENSE00001458628	102126804	102127712
ENSE00001458629	102125679	102125806
ENSE00001707493	102126373	102126445

Expression profiles

Bgee: expression breadth ubiquitous, 247 present calls, max score 99.70.

FANTOM5 (CAGE): breadth broad, TPM avg 10.1865 / max 1693.7265, expressed in 390 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196974	6.1553	368
196975	1.2013	181
209760	0.9173	239
196979	0.5150	101
196976	0.3394	95
196981	0.3227	82
196977	0.2564	73
196980	0.2492	83
196973	0.1338	66
196978	0.0960	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	99.70	gold quality
Brodmann (1909) area 23	UBERON:0013554	99.57	gold quality
middle temporal gyrus	UBERON:0002771	99.25	gold quality
primary visual cortex	UBERON:0002436	99.14	gold quality
nucleus accumbens	UBERON:0001882	98.91	gold quality
occipital lobe	UBERON:0002021	98.91	gold quality
adenohypophysis	UBERON:0002196	98.80	gold quality
cerebellar cortex	UBERON:0002129	98.78	gold quality
pituitary gland	UBERON:0000007	98.77	gold quality
cerebellar hemisphere	UBERON:0002245	98.77	gold quality
right frontal lobe	UBERON:0002810	98.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.73	gold quality
cerebellum	UBERON:0002037	98.72	gold quality
superior vestibular nucleus	UBERON:0007227	98.71	gold quality
superior frontal gyrus	UBERON:0002661	98.70	gold quality
pons	UBERON:0000988	98.69	gold quality
cerebellar vermis	UBERON:0004720	98.68	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.67	gold quality
caudate nucleus	UBERON:0001873	98.66	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.65	gold quality
amygdala	UBERON:0001876	98.59	gold quality
frontal cortex	UBERON:0001870	98.57	gold quality
putamen	UBERON:0001874	98.56	gold quality
hypothalamus	UBERON:0001898	98.56	gold quality
temporal lobe	UBERON:0001871	98.54	gold quality
cortical plate	UBERON:0005343	98.53	gold quality
neocortex	UBERON:0001950	98.52	gold quality
entorhinal cortex	UBERON:0002728	98.50	gold quality
cerebral cortex	UBERON:0000956	98.48	gold quality
anterior cingulate cortex	UBERON:0009835	98.47	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.10
E-GEOD-93593	yes	16.19
E-MTAB-7316	yes	14.15
E-GEOD-84465	yes	7.07
E-ANND-3	yes	6.04
E-HCAD-31	no	546.85
E-GEOD-83139	no	3.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting TCEAL2, 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-10527-5P	99.91	72.28	3754
HSA-MIR-556-3P	99.74	68.75	1203
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-4686	98.77	66.87	964

Literature-anchored findings (GeneRIF, showing 1)

• Characterizes TCEAL1, another member of the human TCEAL gene family. (PMID:10051408)

Cross-species orthologs

0 orthologs

Paralogs (8): TCEAL4 (ENSG00000133142), TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL7 (ENSG00000182916), TCEAL9 (ENSG00000185222), TCEAL3 (ENSG00000196507), TCEAL5 (ENSG00000204065), TCEAL6 (ENSG00000204071)

Protein

Protein identifiers

Transcription elongation factor A protein-like 2 — Q9H3H9 (reviewed: Q9H3H9)

Alternative names: Transcription elongation factor S-II protein-like 2

All UniProt accessions (1): Q9H3H9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the TFS-II family. TFA subfamily.

RefSeq proteins (1): NP_525129* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (10 total): compositionally biased region 5, region of interest 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H3H9-F1	62.04	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): WALLACE_PROSTATE_CANCER_RACE_UP, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, VECCHI_GASTRIC_CANCER_EARLY_DN, SENESE_HDAC3_TARGETS_DN, SMID_BREAST_CANCER_LUMINAL_B_DN, BLALOCK_ALZHEIMERS_DISEASE_DN, HAMAI_APOPTOSIS_VIA_TRAIL_UP, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, LIU_PROSTATE_CANCER_DN, ZHAN_MULTIPLE_MYELOMA_MS_UP, VERHAAK_GLIOBLASTOMA_NEURAL, chrXq22, BMI1_DN_MEL18_DN.V1_DN, BMI1_DN.V1_DN, MEL18_DN.V1_DN

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1506 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEAL2	BEX5	Q5H9J7	575
TCEAL2	TCEAL8	Q8IYN2	490
TCEAL2	BEX2	Q9BXY8	452
TCEAL2	BEX1	Q9HBH7	446
TCEAL2	TCEAL1	Q15170	441
TCEAL2	BEX3	Q00994	438
TCEAL2	TCEAL7	Q9BRU2	399
TCEAL2	BEX4	Q9NWD9	380
TCEAL2	ZNF578	Q96N58	348
TCEAL2	ZNF34	Q8IZ26	322
TCEAL2	RAB40A	Q8WXH6	321
TCEAL2	CPA6	Q8N4T0	315
TCEAL2	VCX3B	Q9H321	314
TCEAL2	KLHDC4	Q8TBB5	305
TCEAL2	PWWP3B	Q5H9M0	301

IntAct

19 interactions, top by confidence:

A	B	Type	Score
TCEAL4	USP11	psi-mi:“MI:0914”(association)	0.530
	TCEAL2	psi-mi:“MI:0407”(direct interaction)	0.440
SRPK1	TCEAL2	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
ERBB2	TCEAL2	psi-mi:“MI:0915”(physical association)	0.370
CUL4B	APBB1	psi-mi:“MI:0914”(association)	0.350
PCDHA12	KLRG2	psi-mi:“MI:0914”(association)	0.350
LRRFIP1	TFR2	psi-mi:“MI:0914”(association)	0.350
USP11	PRRC2B	psi-mi:“MI:0914”(association)	0.350
TCEAL1	PDCD5	psi-mi:“MI:0914”(association)	0.350
SQSTM1	CHEK1	psi-mi:“MI:0914”(association)	0.350
LRRFIP1	CCNB1	psi-mi:“MI:0914”(association)	0.350
TCEAL2	MYL9	psi-mi:“MI:0914”(association)	0.350
TMEM68	MTMR3	psi-mi:“MI:0914”(association)	0.350
NR3C1	TCEAL2	psi-mi:“MI:0915”(physical association)	0.000
PHB1	TCEAL2	psi-mi:“MI:0915”(physical association)	0.000
TCEAL2	TFCP2	psi-mi:“MI:0915”(physical association)	0.000
TCEAL2	NELFB	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (30): TCEAL2 (Two-hybrid), TCEAL2 (Reconstituted Complex), TCEAL2 (Affinity Capture-MS), TCEAL2 (Affinity Capture-MS), TCEAL2 (Affinity Capture-MS), TCEAL2 (Affinity Capture-MS), TCEAL2 (Affinity Capture-MS), MGME1 (Affinity Capture-MS), MYL9 (Affinity Capture-MS), TCEAL2 (Affinity Capture-MS), USP15 (Affinity Capture-MS), CCNY (Affinity Capture-MS), CCNYL1 (Affinity Capture-MS), TCEAL4 (Affinity Capture-MS), USP11 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQG5, A0A1D9BZF0, B3EWZ0, B3EWZ1, B4F777, D3YZV8, O01949, O46383, O75459, P04922, P08116, P13665, P31568, P31569, P32447, P49451, P62521, P82970, Q01033, Q01042, Q02752, Q0ZNK1, Q14093, Q28139, Q2GIB5, Q54RM7, Q5H9L2, Q5MIT9, Q5MJ10, Q5R6B4, Q5SRN2, Q6AXX0, Q6BYE5, Q6CI62, Q6IPX3, Q6SJ82, Q7M3V1, Q7YT37, Q8BGC0, Q8CCT4

Diamond homologs: Q5H9L2, Q5R6B4, Q6IPX3, Q8CCT4, Q8R0A5, Q969E4, Q96EI5, Q9H3H9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

247 predictions. Top by Δscore:

Variant	Effect	Δscore
X:102125777:G:GT	donor_gain	1.0000
X:102125807:G:C	donor_loss	1.0000
X:102126417:G:GT	donor_gain	1.0000
X:102126443:CAGG:C	donor_loss	1.0000
X:102126444:AG:A	donor_loss	1.0000
X:102126445:GGTC:G	donor_loss	1.0000
X:102126446:G:T	donor_loss	1.0000
X:102126791:A:AG	acceptor_gain	1.0000
X:102126792:C:G	acceptor_gain	1.0000
X:102125803:GCAG:G	donor_gain	0.9900
X:102126368:CGCA:C	acceptor_loss	0.9900
X:102126369:GCA:G	acceptor_loss	0.9900
X:102126370:CA:C	acceptor_loss	0.9900
X:102126371:AGGT:A	acceptor_loss	0.9900
X:102126372:G:GT	acceptor_loss	0.9900
X:102126447:T:A	donor_loss	0.9900
X:102126789:A:AG	acceptor_gain	0.9900
X:102126790:C:G	acceptor_gain	0.9900
X:102126364:T:A	acceptor_gain	0.9800
X:102126371:A:AG	acceptor_gain	0.9800
X:102126372:G:GG	acceptor_gain	0.9800
X:102126799:CCCA:C	acceptor_loss	0.9800
X:102126800:CCAG:C	acceptor_loss	0.9800
X:102126803:G:T	acceptor_loss	0.9800
X:102126372:GGTCT:G	acceptor_gain	0.9700
X:102126487:GGT:G	donor_gain	0.9700
X:102126460:G:GT	donor_gain	0.9600
X:102126796:T:G	acceptor_gain	0.9600
X:102125810:A:AG	donor_gain	0.9500
X:102125811:G:GG	donor_gain	0.9500

AlphaMissense

1515 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:102127250:A:C	R140S	0.981
X:102127250:A:T	R140S	0.981
X:102127296:G:C	A156P	0.981
X:102127434:T:C	F202L	0.978
X:102127436:C:A	F202L	0.978
X:102127436:C:G	F202L	0.978
X:102127253:A:C	K141N	0.973
X:102127253:A:T	K141N	0.973
X:102127341:T:C	F171L	0.968
X:102127343:T:A	F171L	0.968
X:102127343:T:G	F171L	0.968
X:102127407:T:A	W193R	0.968
X:102127407:T:C	W193R	0.968
X:102127463:G:C	R211S	0.968
X:102127463:G:T	R211S	0.968
X:102127292:G:C	K154N	0.966
X:102127292:G:T	K154N	0.966
X:102127247:A:C	K139N	0.965
X:102127247:A:T	K139N	0.965
X:102127255:C:T	T142I	0.963
X:102127446:G:C	G206R	0.963
X:102127252:A:T	K141I	0.960
X:102127454:G:C	R208S	0.958
X:102127454:G:T	R208S	0.958
X:102127300:T:A	I157K	0.956
X:102127411:T:C	M194T	0.953
X:102127409:G:C	W193C	0.952
X:102127409:G:T	W193C	0.952
X:102127445:G:C	R205S	0.951
X:102127445:G:T	R205S	0.951

dbSNP variants (sampled 300 via entrez): RS1002652533 (X:102123699 T>C), RS1002947265 (X:102123855 A>T), RS1003859511 (X:102128128 G>C), RS1004756457 (X:102127132 A>G), RS1009060999 (X:102125668 G>A), RS1010964904 (X:102125686 C>T), RS1011079716 (X:102126077 A>T), RS1012206578 (X:102126651 G>C), RS1012538815 (X:102124444 A>G), RS1015555338 (X:102124496 T>C), RS1016467591 (X:102124504 A>G), RS1017701249 (X:102125326 G>A), RS1017817482 (X:102125671 C>A), RS1021091248 (X:102123770 G>A,T), RS1022384210 (X:102126096 T>A,C,G)

Disease associations

OMIM: gene MIM:301152 | 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
GCST90000047_270	Age at first sexual intercourse	5.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
trichostatin A	increases expression	2
mercuric bromide	decreases expression, affects cotreatment	2
Benzo(a)pyrene	decreases methylation, increases expression, affects methylation	2
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Aflatoxin B1	affects expression, decreases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
titanium dioxide	decreases expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
Decitabine	affects expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	affects expression	1
Thimerosal	decreases expression	1
Tretinoin	decreases expression	1
Triclosan	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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