TCEANC

Summary

TCEANC (transcription elongation factor A N-terminal and central domain containing, HGNC:28277) is a protein-coding gene on chromosome Xp22.2, encoding Transcription elongation factor A N-terminal and central domain-containing protein (Q8N8B7).

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

Source: NCBI Gene 170082 — RefSeq curated summary.

At a glance

• Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited, GenCC)
• Clinical variants (ClinVar): 52 total — 1 pathogenic
• MANE Select transcript: NM_001297563

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28277
Approved symbol	TCEANC
Name	transcription elongation factor A N-terminal and central domain containing
Location	Xp22.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC17403, TCEANC1
Ensembl gene	ENSG00000176896
Ensembl biotype	protein_coding
OMIM	301084
Entrez	170082

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 27 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000380600, ENST00000463321, ENST00000467590, ENST00000490617, ENST00000544987, ENST00000696126, ENST00000696127, ENST00000696128, ENST00000696129, ENST00000696130, ENST00000880871, ENST00000880872, ENST00000880873, ENST00000880874, ENST00000880875, ENST00000880876, ENST00000934380, ENST00000934381, ENST00000934382, ENST00000934383, ENST00000934384, ENST00000934385, ENST00000934386, ENST00000961748, ENST00000961749, ENST00000961750, ENST00000961751, ENST00000961752, ENST00000961753

RefSeq mRNA: 3 — MANE Select: NM_001297563 NM_001297563, NM_001297564, NM_152634

CCDS: CCDS48081, CCDS75954

Canonical transcript exons

ENST00000696128 — 5 exons

Exon	Start	End
ENSE00003966075	13653141	13653188
ENSE00003966083	13662501	13665409
ENSE00003966088	13661031	13661122
ENSE00003966092	13659652	13659768
ENSE00003966093	13655289	13655373

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 80.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.8423 / max 108.6505, expressed in 1076 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195575	2.8423	1076

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	80.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.09	gold quality
calcaneal tendon	UBERON:0003701	77.99	gold quality
bone marrow cell	CL:0002092	77.51	gold quality
sural nerve	UBERON:0015488	75.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	73.35	gold quality
islet of Langerhans	UBERON:0000006	72.44	gold quality
leukocyte	CL:0000738	72.41	gold quality
apex of heart	UBERON:0002098	72.39	gold quality
colonic epithelium	UBERON:0000397	72.32	silver quality
ventricular zone	UBERON:0003053	72.26	gold quality
secondary oocyte	CL:0000655	72.05	gold quality
muscle of leg	UBERON:0001383	71.79	gold quality
monocyte	CL:0000576	71.76	gold quality
ganglionic eminence	UBERON:0004023	71.56	gold quality
bone marrow	UBERON:0002371	71.24	gold quality
cortical plate	UBERON:0005343	71.22	gold quality
gastrocnemius	UBERON:0001388	71.20	gold quality
right lobe of liver	UBERON:0001114	70.72	gold quality
cerebellar hemisphere	UBERON:0002245	70.48	gold quality
lymph node	UBERON:0000029	70.47	gold quality
cerebellar cortex	UBERON:0002129	70.35	gold quality
smooth muscle tissue	UBERON:0001135	70.26	gold quality
spleen	UBERON:0002106	70.04	gold quality
stromal cell of endometrium	CL:0002255	70.02	gold quality
blood	UBERON:0000178	70.02	gold quality
vermiform appendix	UBERON:0001154	69.94	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.54	gold quality
pancreas	UBERON:0001264	69.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.59
E-MTAB-9801	no	2.97

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting TCEANC, 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-8485	100.00	77.57	4731
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-12130	99.75	65.47	452
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-3618	99.69	68.57	1012

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000115856
mus_musculus	Tceanc	ENSMUSG00000051224
rattus_norvegicus	Tceanc	ENSRNOG00000065918

Paralogs (3): TCEA2 (ENSG00000171703), TCEA1 (ENSG00000187735), TCEA3 (ENSG00000204219)

Protein

Protein identifiers

Transcription elongation factor A N-terminal and central domain-containing protein — Q8N8B7 (reviewed: Q8N8B7)

Alternative names: TFIIS central domain-containing protein 1

All UniProt accessions (3): A0A8Q3SID2, Q8N8B7, H0YF26

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N8B7-1	1	yes
Q8N8B7-2	2

RefSeq proteins (3): NP_001284492, NP_001284493, NP_689847 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003618	TFIIS_cen_dom	Domain
IPR017923	TFIIS_N	Domain
IPR035100	TF_IIS-typ	Family
IPR035441	TFIIS/LEDGF_dom_sf	Homologous_superfamily
IPR036575	TFIIS_cen_dom_sf	Homologous_superfamily

Pfam: PF07500, PF08711

UniProt features (9 total): domain 2, region of interest 2, compositionally biased region 2, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8B7-F1	72.35	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): ZHANG_BREAST_CANCER_PROGENITORS_UP, GOBP_DNA_TEMPLATED_TRANSCRIPTION_ELONGATION, chrXp22, DUAN_PRDM5_TARGETS, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FOXJ2_TARGET_GENES, HES2_TARGET_GENES, MAFG_TARGET_GENES, SOX3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF423_TARGET_GENES, ZNF577_TARGET_GENES, ZNF660_TARGET_GENES, MIR5696, LET_7C_3P

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

1156 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCEANC	GEMIN8	Q9NWZ8	716
TCEANC	TRAPPC2	P0DI81	612
TCEANC	PNPLA4	P41247	567
TCEANC	EGFL6	Q8IUX8	561
TCEANC	CTPS2	Q9NRF8	534
TCEANC	MED14	O60244	523
TCEANC	RPS4X	P12631	490
TCEANC	KDM5C	P41229	472
TCEANC	KRABD4	Q5JUW0	447
TCEANC	ARSF	P54793	438
TCEANC	RIBC1	Q8N443	427
TCEANC	BRCA1	P38398	427
TCEANC	CXorf38	Q8TB03	419
TCEANC	ZNF492	Q9P255	405
TCEANC	CTCF	P49711	396

IntAct

77 interactions, top by confidence:

A	B	Type	Score
TCEANC	FSD2	psi-mi:“MI:0915”(physical association)	0.560
MID1	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	SSNA1	psi-mi:“MI:0915”(physical association)	0.560
ZBTB14	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
DAB1	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
FSBP	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-9	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
MEOX1	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.560
GOLGA2	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	VAC14	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	TARBP2	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	NAB2	psi-mi:“MI:0915”(physical association)	0.560
OBI1	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	HMBOX1	psi-mi:“MI:0915”(physical association)	0.560
FAM9B	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
VPS52	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	CRACR2B	psi-mi:“MI:0915”(physical association)	0.560
CBY2	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	PNMA1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	CSRNP1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	KIFC3	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-2	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
CARD9	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
FSD2	TCEANC	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	MID1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	DAB1	psi-mi:“MI:0915”(physical association)	0.560
TCEANC	FSBP	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (168): TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid), TCEANC (Two-hybrid)

ESM2 similar proteins: A0A1L8HU22, A1A5R8, A8K979, B8A5Y1, E1BB03, F6UH96, O75113, P62283, P62285, P62286, P62287, P62288, P62289, P62290, P62291, P62292, P62293, P62294, P62296, P62297, Q08AX9, Q3MHN7, Q3US16, Q5BKS4, Q5HZL1, Q5XKL5, Q5ZIX8, Q5ZLE9, Q64702, Q68FF0, Q6A037, Q6IE81, Q6NQ79, Q6NSI8, Q6NZP1, Q6PCM1, Q8BMI4, Q8BVE8, Q8BZ05, Q8CJ27

Diamond homologs: B0UYI1, F4J4Y5, O75764, P07273, P0C8F5, P0C8F6, P0C8F7, P0C8F8, P10711, P20232, P23193, P23881, P27948, P49373, P52652, Q04307, Q07271, Q148K0, Q15560, Q29RL9, Q2KI09, Q2M2S7, Q3US16, Q4KLL0, Q54YG9, Q5UQS8, Q63799, Q6GZP4, Q8C9B9, Q8N8B7, Q90YL3, Q92576, Q9BTC0, Q9CQZ7, Q9FHK9, Q9GMV6, Q9QVN7, Q9Y2Y1, Q9ZVH8, A5PK23

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	36
Likely benign	8
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
816269	GRCh37/hg19 Xp22.33-22.11(chrX:537158-22883547)x1	Pathogenic

SpliceAI

154 predictions. Top by Δscore:

Variant	Effect	Δscore
X:13662499:A:AG	acceptor_gain	1.0000
X:13662500:G:GA	acceptor_gain	1.0000
X:13662500:GC:G	acceptor_gain	1.0000
X:13662500:GCT:G	acceptor_gain	1.0000
X:13662500:GCTGT:G	acceptor_gain	1.0000
X:13660618:ACT:A	donor_gain	0.9900
X:13662496:TGCA:T	acceptor_loss	0.9900
X:13662497:GCA:G	acceptor_loss	0.9900
X:13662498:CA:C	acceptor_loss	0.9900
X:13662499:AGCT:A	acceptor_gain	0.9900
X:13662500:GCTG:G	acceptor_gain	0.9900
X:13659722:TTC:T	donor_gain	0.9200
X:13659764:TACAG:T	donor_loss	0.9200
X:13659765:ACAG:A	donor_loss	0.9200
X:13659767:AG:A	donor_loss	0.9200
X:13659768:GG:G	donor_loss	0.9200
X:13659769:G:GC	donor_loss	0.9200
X:13659770:T:A	donor_loss	0.9200
X:13662502:T:A	acceptor_gain	0.9000
X:13662496:TGCAG:T	acceptor_gain	0.8700
X:13662496:T:TA	acceptor_gain	0.8600
X:13660619:C:G	donor_gain	0.8500
X:13662499:AGC:A	acceptor_gain	0.8200
X:13662215:TGGAA:T	donor_gain	0.8100
X:13659769:G:GG	donor_gain	0.7900
X:13662241:C:T	donor_gain	0.7800
X:13662502:TGTAA:T	acceptor_gain	0.7700
X:13662498:CAG:C	acceptor_gain	0.7600
X:13662497:GCAGC:G	acceptor_gain	0.7300
X:13662260:T:G	donor_gain	0.7200

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000272725 (X:13661471 T>C), RS1000425709 (X:13653525 A>G), RS1000494438 (X:13663993 C>T), RS1000563321 (X:13654123 C>T), RS1000862401 (X:13653223 C>G,T), RS1001174690 (X:13655920 G>A), RS1002439127 (X:13657645 T>A), RS1002880279 (X:13657326 T>C), RS1002891176 (X:13651214 A>G), RS1003256375 (X:13652842 T>C,G), RS1003759429 (X:13658502 G>A), RS1004379102 (X:13657286 G>T), RS1004484125 (X:13665300 T>C), RS1004586351 (X:13664921 C>A,G), RS1004651328 (X:13653878 A>C)

Disease associations

OMIM: gene MIM:301084 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
male infertility with azoospermia or oligozoospermia due to single gene mutation	Limited	X-linked

Mondo (1): (MONDO:0018393)

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

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
alpha phellandrene	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
hydroquinone	decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Cadmium	increases abundance, increases expression	1
Cisplatin	increases expression	1
Endosulfan	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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