TCEANC2

Summary

TCEANC2 (transcription elongation factor A N-terminal and central domain containing 2, HGNC:26494) is a protein-coding gene on chromosome 1p32.3, encoding Transcription elongation factor A N-terminal and central domain-containing protein 2 (Q96MN5).

Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 127428 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 26 total
• MANE Select transcript: NM_153035

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26494
Approved symbol	TCEANC2
Name	transcription elongation factor A N-terminal and central domain containing 2
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32112
Ensembl gene	ENSG00000116205
Ensembl biotype	protein_coding
Entrez	127428

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000234827, ENST00000371331, ENST00000391366, ENST00000498272, ENST00000648983, ENST00000858858, ENST00000932812

RefSeq mRNA: 1 — MANE Select: NM_153035 NM_153035

CCDS: CCDS587

Canonical transcript exons

ENST00000234827 — 5 exons

Exon	Start	End
ENSE00000772708	54068756	54068897
ENSE00001064661	54096285	54106082
ENSE00001346720	54053608	54053758
ENSE00003466307	54088597	54088790
ENSE00003503445	54054381	54054524

Expression profiles

Bgee: expression breadth ubiquitous, 173 present calls, max score 81.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2780 / max 177.2784, expressed in 1772 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2937	5.6558	1731
2938	1.6223	763

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	81.33	gold quality
male germ cell	CL:0000015	78.72	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.18	gold quality
monocyte	CL:0000576	75.97	gold quality
mononuclear cell	CL:0000842	75.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.65	gold quality
leukocyte	CL:0000738	75.58	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	75.51	gold quality
spinal cord	UBERON:0002240	74.45	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	74.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.64	gold quality
granulocyte	CL:0000094	73.17	gold quality
lateral nuclear group of thalamus	UBERON:0002736	72.99	gold quality
gastrocnemius	UBERON:0001388	72.97	gold quality
muscle of leg	UBERON:0001383	72.85	gold quality
lateral globus pallidus	UBERON:0002476	72.68	gold quality
ganglionic eminence	UBERON:0004023	72.56	gold quality
stromal cell of endometrium	CL:0002255	72.50	gold quality
cortical plate	UBERON:0005343	72.07	gold quality
substantia nigra pars reticulata	UBERON:0001966	72.04	gold quality
rectum	UBERON:0001052	71.93	gold quality
ventricular zone	UBERON:0003053	71.88	gold quality
lymph node	UBERON:0000029	71.69	gold quality
vena cava	UBERON:0004087	71.52	gold quality
amygdala	UBERON:0001876	71.46	gold quality
right testis	UBERON:0004534	71.34	gold quality
left testis	UBERON:0004533	71.27	gold quality
skeletal muscle organ	UBERON:0014892	70.41	gold quality
muscle organ	UBERON:0001630	70.40	gold quality
testis	UBERON:0000473	70.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

205 targeting TCEANC2, 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-3646	100.00	73.56	5283
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	tceanc2	ENSDARG00000062919
mus_musculus	Tceanc2	ENSMUSG00000028619
rattus_norvegicus	Tceanc2	ENSRNOG00000009398

Protein

Protein identifiers

Transcription elongation factor A N-terminal and central domain-containing protein 2 — Q96MN5 (reviewed: Q96MN5)

All UniProt accessions (3): A0A0D9SFA7, Q96MN5, X6R7X0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the TCEANC2 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96MN5-1	1	yes
Q96MN5-2	2

RefSeq proteins (1): NP_694580* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003617	TFIIS/CRSP70_N_sub	Domain
IPR003618	TFIIS_cen_dom	Domain
IPR017923	TFIIS_N	Domain
IPR035441	TFIIS/LEDGF_dom_sf	Homologous_superfamily
IPR036575	TFIIS_cen_dom_sf	Homologous_superfamily

Pfam: PF08711

UniProt features (7 total): domain 2, chain 1, region of interest 1, modified residue 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MN5-F1	85.22	0.37

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 (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 112 (showing top): FREAC4_01, CUI_TCF21_TARGETS_2_DN, CCAGGGG_MIR331, NUYTTEN_EZH2_TARGETS_DN, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, SCGGAAGY_ELK1_02, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, STAT5A_02, CCTGAGT_MIR510, GOBP_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION, BRUINS_UVC_RESPONSE_EARLY_LATE, SNACANNNYSYAGA_UNKNOWN, ZWANG_DOWN_BY_2ND_EGF_PULSE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

GO Biological Process (2): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357)

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
gene expression	1
RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEANC2	HDHD5	Q9BXW7	566
TCEANC2	LRRC38	Q5VT99	523
TCEANC2	TACO1	Q9BSH4	468
TCEANC2	TCEA1	P23193	450
TCEANC2	CCDC117	Q8IWD4	450
TCEANC2	MRPL16	Q9NX20	446
TCEANC2	PSTK	Q8IV42	432
TCEANC2	FBXO48	Q5FWF7	418
TCEANC2	PUDP	Q08623	417
TCEANC2	MPHOSPH10	O00566	416
TCEANC2	LDLRAD1	Q5T700	407
TCEANC2	ZNF773	Q6PK81	400
TCEANC2	TCEAL8	Q8IYN2	392
TCEANC2	EIF2B3	Q9NR50	387
TCEANC2	RASL10B	Q96S79	383

IntAct

18 interactions, top by confidence:

A	B	Type	Score
TNIP1	TCEANC2	psi-mi:“MI:0915”(physical association)	0.670
TCEANC2	TNIP1	psi-mi:“MI:0915”(physical association)	0.670
TCEANC2	AGTRAP	psi-mi:“MI:0915”(physical association)	0.560
AGTRAP	TCEANC2	psi-mi:“MI:0915”(physical association)	0.560
TCEANC2	PICK1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC2	HTATSF1	psi-mi:“MI:0914”(association)	0.530
TCEANC2	H1-4	psi-mi:“MI:0915”(physical association)	0.400
TCEANC2	SPRING1	psi-mi:“MI:0915”(physical association)	0.400
HIF1A	PIAS1	psi-mi:“MI:0914”(association)	0.350
TCEANC2	ANKHD1	psi-mi:“MI:0914”(association)	0.350
	POLRMT	psi-mi:“MI:0914”(association)	0.350
TCEANC2	AGRN	psi-mi:“MI:0914”(association)	0.350
TCEANC2	PICK1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (48): TCEANC2 (Two-hybrid), TCEANC2 (Two-hybrid), TCEANC2 (Reconstituted Complex), TCEANC2 (Biochemical Activity), TCEANC2 (Affinity Capture-MS), UBE2R2 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), UBXN7 (Affinity Capture-MS), CDC34 (Affinity Capture-MS), ANKHD1-EIF4EBP3 (Affinity Capture-MS), FAM21A (Affinity Capture-MS), DCAF16 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), PHKA2 (Affinity Capture-MS)

ESM2 similar proteins: A1Z3X3, A2AT37, A4GWN3, A5PKE4, B0UYI1, B2GV38, O08848, O35841, O43395, O75031, P49754, Q08CZ0, Q15397, Q15650, Q2HJ41, Q2T9K6, Q3UBZ5, Q5EAQ1, Q5KU39, Q5R5F1, Q5R644, Q5RCR8, Q5RE03, Q5U3V9, Q5VZK9, Q5XIC7, Q5ZJ85, Q5ZKG8, Q5ZMW3, Q676U5, Q6GLK9, Q6GMH0, Q6NYU2, Q7Z3V4, Q80UM3, Q80YQ8, Q8BHL5, Q8BM39, Q8R2M0, Q8WV92

Diamond homologs: A5PKE4, B0UYI1, F4J4Y5, Q5XIC7, Q8R2M0, Q96MN5, Q9FHK9, O75764, P10711, P20232, P23193, P23881, Q148K0, Q29RL9, Q4KLL0, Q14241, Q2KI09, Q63187, Q8CB77, O13896, P07273, P0C8F5, P0C8F6, P0C8F7, P0C8F8, P27948, P49373, P52652, Q04307, Q07271, Q15560, Q197A5, Q2M2S7, Q54YG9, Q56254, Q5JF34, Q5UQS8, Q63799, Q6GZP4, Q980K2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1109 predictions. Top by Δscore:

Variant	Effect	Δscore
1:54053659:G:GT	donor_gain	1.0000
1:54053738:C:G	donor_gain	1.0000
1:54054520:TGAAG:T	donor_loss	1.0000
1:54054521:GAAGG:G	donor_loss	1.0000
1:54054522:AAGG:A	donor_loss	1.0000
1:54054523:AGGTG:A	donor_loss	1.0000
1:54054524:GG:G	donor_loss	1.0000
1:54054525:G:A	donor_loss	1.0000
1:54054526:T:G	donor_loss	1.0000
1:54068755:GAGA:G	acceptor_gain	1.0000
1:54068873:G:GT	donor_gain	1.0000
1:54068873:G:T	donor_gain	1.0000
1:54068892:GGA:G	donor_gain	1.0000
1:54068893:GA:G	donor_gain	1.0000
1:54068894:A:G	donor_gain	1.0000
1:54088589:T:TA	acceptor_gain	1.0000
1:54088593:CCA:C	acceptor_loss	1.0000
1:54088594:CA:C	acceptor_loss	1.0000
1:54088595:A:AG	acceptor_gain	1.0000
1:54088596:G:GA	acceptor_gain	1.0000
1:54088596:GGT:G	acceptor_gain	1.0000
1:54088596:GGTC:G	acceptor_gain	1.0000
1:54088596:GGTCA:G	acceptor_gain	1.0000
1:54088786:TAAAG:T	donor_loss	1.0000
1:54088787:AAAGG:A	donor_loss	1.0000
1:54088791:GTAAT:G	donor_loss	1.0000
1:54088792:T:G	donor_loss	1.0000
1:54053756:CTGGT:C	donor_loss	0.9900
1:54053757:TGGTG:T	donor_loss	0.9900
1:54053758:GGTG:G	donor_loss	0.9900

AlphaMissense

1343 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:54088671:T:A	W107R	0.996
1:54088671:T:C	W107R	0.996
1:54088673:G:C	W107C	0.989
1:54088673:G:T	W107C	0.989
1:54068850:T:C	L66S	0.986
1:54088651:C:A	A100D	0.986
1:54088606:T:A	V85E	0.985
1:54088748:G:C	R132S	0.983
1:54088748:G:T	R132S	0.983
1:54054432:T:C	F4L	0.982
1:54054434:C:A	F4L	0.982
1:54054434:C:G	F4L	0.982
1:54088672:G:C	W107S	0.981
1:54096379:T:C	L178P	0.980
1:54068895:T:A	I81K	0.979
1:54096324:T:C	F160L	0.978
1:54096326:T:A	F160L	0.978
1:54096326:T:G	F160L	0.978
1:54096374:A:C	R176S	0.978
1:54096374:A:T	R176S	0.978
1:54096364:G:C	R173P	0.977
1:54054516:T:C	S32P	0.976
1:54088747:G:C	R132T	0.976
1:54096384:T:C	F180L	0.975
1:54096386:C:A	F180L	0.975
1:54096386:C:G	F180L	0.975
1:54068763:T:A	V37E	0.974
1:54054511:T:A	I30N	0.973
1:54068760:T:A	V36D	0.973
1:54096361:G:C	R172P	0.973

dbSNP variants (sampled 300 via entrez): RS1000014217 (1:54076161 G>T), RS1000082212 (1:54084021 T>A,G), RS1000133245 (1:54083737 T>C), RS1000151020 (1:54075756 C>G), RS1000235823 (1:54051805 T>C), RS1000241300 (1:54097066 T>G), RS1000245109 (1:54083057 A>G), RS1000258068 (1:54076956 C>A), RS1000385286 (1:54105695 T>C), RS1000389373 (1:54098049 A>G), RS1000455349 (1:54052150 T>C), RS1000493559 (1:54052253 GA>G), RS1000571400 (1:54095644 T>C), RS1000689871 (1:54071837 G>A,T), RS1000769214 (1:54095877 T>C)

Disease associations

OMIM: gene `` | 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
GCST002778_2	Parkinson disease and lewy body pathology	6.000000e-08

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Resveratrol	increases expression, affects cotreatment	1
Acetaminophen	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	affects expression	1
Doxorubicin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Triclosan	decreases expression	1
Asbestos, Serpentine	affects methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases methylation	1

Clinical trials (associated diseases)

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