TCEAL6

Summary

TCEAL6 (transcription elongation factor A like 6, HGNC:24553) is a protein-coding gene on chromosome Xq22.1, encoding Transcription elongation factor A protein-like 6 (Q6IPX3). May be involved in transcriptional regulation.

Predicted to be located in nucleus.

Source: NCBI Gene 158931 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 27 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24553
Approved symbol	TCEAL6
Name	transcription elongation factor A like 6
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Aliases	WEX2
Ensembl gene	ENSG00000204071
Ensembl biotype	protein_coding
OMIM	301156
Entrez	158931

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000372773, ENST00000372774

RefSeq mRNA: 1 — MANE Select: None NM_001006938

Canonical transcript exons

ENST00000372773 — 4 exons

Exon	Start	End
ENSE00001458615	102140812	102141350
ENSE00001458616	102142702	102142970
ENSE00001777097	102141714	102141786
ENSE00003923721	102140710	102140809

Expression profiles

Bgee: expression breadth ubiquitous, 116 present calls, max score 96.34.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.9387 / max 86.1217, expressed in 119 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
199970	0.9387	119

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
superior frontal gyrus	UBERON:0002661	96.34	gold quality
cerebellar cortex	UBERON:0002129	96.22	gold quality
cerebellum	UBERON:0002037	96.20	gold quality
cerebellar hemisphere	UBERON:0002245	96.20	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.12	gold quality
hypothalamus	UBERON:0001898	95.99	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.59	gold quality
primary visual cortex	UBERON:0002436	95.58	gold quality
frontal cortex	UBERON:0001870	95.43	gold quality
right frontal lobe	UBERON:0002810	95.39	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.36	gold quality
pituitary gland	UBERON:0000007	95.33	gold quality
prefrontal cortex	UBERON:0000451	95.32	gold quality
adenohypophysis	UBERON:0002196	94.98	gold quality
anterior cingulate cortex	UBERON:0009835	94.32	gold quality
cerebral cortex	UBERON:0000956	94.25	gold quality
brain	UBERON:0000955	93.93	gold quality
nucleus accumbens	UBERON:0001882	93.49	gold quality
temporal lobe	UBERON:0001871	93.31	gold quality
amygdala	UBERON:0001876	93.30	gold quality
substantia nigra	UBERON:0002038	93.11	gold quality
caudate nucleus	UBERON:0001873	91.74	gold quality
putamen	UBERON:0001874	91.11	gold quality
Ammon’s horn	UBERON:0001954	90.58	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.05	gold quality
right testis	UBERON:0004534	87.75	gold quality
left testis	UBERON:0004533	86.19	gold quality
testis	UBERON:0000473	86.16	gold quality
mucosa of stomach	UBERON:0001199	81.51	gold quality
ganglionic eminence	UBERON:0004023	78.44	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.02
E-GEOD-84465	yes	6.52

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

49 targeting TCEAL6, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-221-5P	99.86	65.45	1052
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-548M	99.70	68.87	1749
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-216A-5P	99.50	68.02	1288
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-208A-5P	99.42	70.83	1913
HSA-MIR-208B-5P	99.42	70.83	1952
HSA-MIR-145-3P	99.33	67.66	764

Literature-anchored findings (GeneRIF, showing 1)

• hsa_circ_0101119 facilitates the progression of cervical cancer via an interaction with EIF4A3 to inhibit TCEAL6 expression. (PMID:34278492)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Tceal6	ENSMUSG00000031409
mus_musculus	Tceal3	ENSMUSG00000044550
mus_musculus	Tceal5	ENSMUSG00000054034
rattus_norvegicus	Tceal5	ENSRNOG00000046280
rattus_norvegicus	Tceal6	ENSRNOG00000046390
rattus_norvegicus	Tceal3	ENSRNOG00000049020

Paralogs (8): TCEAL4 (ENSG00000133142), TCEAL1 (ENSG00000172465), TCEAL8 (ENSG00000180964), TCEAL7 (ENSG00000182916), TCEAL2 (ENSG00000184905), TCEAL9 (ENSG00000185222), TCEAL3 (ENSG00000196507), TCEAL5 (ENSG00000204065)

Protein

Protein identifiers

Transcription elongation factor A protein-like 6 — Q6IPX3 (reviewed: Q6IPX3)

Alternative names: Transcription elongation factor S-II protein-like 6

All UniProt accessions (1): Q6IPX3

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6IPX3-1	1	yes
Q6IPX3-2	2

RefSeq proteins (1): NP_001006939 (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021156	TF_A-like/BEX	Family

Pfam: PF04538

UniProt features (9 total): compositionally biased region 4, modified residue 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IPX3-F1	58.70	0.00

Functional residue map

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

Post-translational modifications (2): 30, 65

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): chrXq22, MIR30D_3P, MIR30E_3P, MIR30A_3P, MIR4517, MIR4744, MIR216A_5P, MIR489_3P, MIR6753_5P, SMN1_SMN2_TARGET_GENES, MURARO_PANCREAS_DELTA_CELL, BENPORATH_SUZ12_TARGETS

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

0 interactions, top by confidence (×1000):

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
TCEAL6	SMAD2	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A1L429, A6NDE8, A6NER3, A6NGK3, O41801, O55777, O60829, O75459, O76087, P03204, P04611, P06937, P0CL80, P0CL81, P0CL82, P0DSO3, P0DTW1, P18804, P22421, P86478, P86479, P86480, P86481, P86496, Q13066, Q13069, Q13070, Q2T9P9, Q3KST0, Q4V321, Q4V326, Q5JRK9, Q5JUK9, Q6AY45, Q6I7R5, Q6IPX3, Q6NT46, Q7Z2X7, Q8AIH8, 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	20
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

272 predictions. Top by Δscore:

Variant	Effect	Δscore
X:102141351:CTGTC:C	acceptor_gain	1.0000
X:102141354:TCCTG:T	acceptor_loss	1.0000
X:102141355:CCT:C	acceptor_loss	1.0000
X:102141356:C:A	acceptor_loss	1.0000
X:102141357:T:A	acceptor_loss	1.0000
X:102141363:A:AC	acceptor_gain	1.0000
X:102141367:CAG:C	acceptor_gain	1.0000
X:102141368:A:T	acceptor_gain	1.0000
X:102141369:G:C	acceptor_gain	1.0000
X:102141369:G:GC	acceptor_gain	1.0000
X:102141710:GGACC:G	donor_loss	1.0000
X:102141711:GAC:G	donor_loss	1.0000
X:102141713:C:A	donor_loss	1.0000
X:102141741:T:TA	donor_gain	1.0000
X:102141352:TGTC:T	acceptor_gain	0.9900
X:102141354:TC:T	acceptor_gain	0.9900
X:102141355:CC:C	acceptor_gain	0.9900
X:102141356:C:CC	acceptor_gain	0.9900
X:102141363:A:C	acceptor_gain	0.9900
X:102141698:C:CA	donor_gain	0.9900
X:102141785:ACCTG:A	acceptor_loss	0.9900
X:102141786:CCT:C	acceptor_loss	0.9900
X:102141787:C:CC	acceptor_gain	0.9900
X:102141787:C:CG	acceptor_loss	0.9900
X:102141788:T:C	acceptor_loss	0.9900
X:102142349:TGACC:T	donor_loss	0.9900
X:102142350:GACCT:G	donor_loss	0.9900
X:102142352:C:CT	donor_loss	0.9900
X:102141353:GTC:G	acceptor_gain	0.9800
X:102141356:C:T	acceptor_gain	0.9800

AlphaMissense

1212 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003094769 (X:102144155 T>C), RS1003834446 (X:102139390 A>G), RS1006282966 (X:102144134 A>G), RS1007411663 (X:102143383 C>T), RS1007918859 (X:102143683 G>A), RS1009183059 (X:102138722 A>C,G), RS1009500308 (X:102138269 G>A), RS1010822725 (X:102140278 G>T), RS1015491064 (X:102138739 T>G), RS1018776391 (X:102143685 T>C), RS1019419341 (X:102143386 C>T), RS1022232016 (X:102140318 A>T), RS1022964323 (X:102144137 A>G), RS1023415241 (X:102143778 A>G), RS1026264188 (X:102143452 A>G)

Disease associations

OMIM: gene MIM:301156 | 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: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases expression	1
Estradiol	affects expression	1
Plant Extracts	affects cotreatment, increases expression	1
Valproic Acid	increases expression	1

Clinical trials (associated diseases)

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