TCF24

Summary

TCF24 (transcription factor 24, HGNC:32275) is a protein-coding gene on chromosome 8q13.1, encoding Transcription factor 24 (Q7RTU0). Putative transcription factor.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in developmental process and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 100129654 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 33 total
• MANE Select transcript: NM_001193502

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32275
Approved symbol	TCF24
Name	transcription factor 24
Location	8q13.1
Locus type	gene with protein product
Status	Approved
Aliases	bHLHa25
Ensembl gene	ENSG00000261787
Ensembl biotype	protein_coding
Entrez	100129654

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000563496, ENST00000566129, ENST00000929798, ENST00000929799, ENST00000961614, ENST00000961615, ENST00000961616

RefSeq mRNA: 1 — MANE Select: NM_001193502 NM_001193502

CCDS: CCDS59103

Canonical transcript exons

ENST00000563496 — 4 exons

Exon	Start	End
ENSE00002576651	66961376	66961788
ENSE00002587628	66962329	66962591
ENSE00002619575	66946501	66948164
ENSE00002629006	66961877	66961987

Expression profiles

Bgee: expression breadth broad, 67 present calls, max score 78.75.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1880 / max 17.9522, expressed in 62 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
93427	0.1880	62

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.75	silver quality
right uterine tube	UBERON:0001302	63.25	gold quality
islet of Langerhans	UBERON:0000006	59.83	gold quality
heart left ventricle	UBERON:0002084	58.69	gold quality
cardiac ventricle	UBERON:0002082	58.07	gold quality
right atrium auricular region	UBERON:0006631	55.56	gold quality
cardiac atrium	UBERON:0002081	55.16	gold quality
lower lobe of lung	UBERON:0008949	53.85	silver quality
heart	UBERON:0000948	53.15	gold quality
hindlimb stylopod muscle	UBERON:0004252	53.09	gold quality
right testis	UBERON:0004534	51.72	gold quality
mucosa of stomach	UBERON:0001199	51.63	gold quality
apex of heart	UBERON:0002098	51.17	gold quality
adult mammalian kidney	UBERON:0000082	50.49	gold quality
testis	UBERON:0000473	50.24	gold quality
left testis	UBERON:0004533	49.68	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	48.21	gold quality
skeletal muscle tissue	UBERON:0001134	47.55	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	47.40	gold quality
muscle of leg	UBERON:0001383	46.47	gold quality
gastrocnemius	UBERON:0001388	46.36	gold quality
kidney	UBERON:0002113	45.95	gold quality
fallopian tube	UBERON:0003889	45.90	gold quality
muscle tissue	UBERON:0002385	45.52	gold quality
skin of hip	UBERON:0001554	45.34	gold quality
body of stomach	UBERON:0001161	45.10	gold quality
nasal cavity mucosa	UBERON:0001826	44.29	gold quality
stomach	UBERON:0000945	44.00	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

84 targeting TCF24, 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-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-548AR-3P	99.85	71.26	3889

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	TCF24	ENSDARG00000086944
mus_musculus	Tcf24	ENSMUSG00000099032
rattus_norvegicus	Tcf24	ENSRNOG00000087348
drosophila_melanogaster	twi	FBGN0003900
drosophila_melanogaster	HLH54F	FBGN0022740
drosophila_melanogaster	Hand	FBGN0032209
drosophila_melanogaster	CG33557	FBGN0053557
caenorhabditis_elegans		WBGENE00001953

Paralogs (13): HAND1 (ENSG00000113196), TCF21 (ENSG00000118526), TWIST1 (ENSG00000122691), TCF15 (ENSG00000125878), FERD3L (ENSG00000146618), TCF23 (ENSG00000163792), HAND2 (ENSG00000164107), PTF1A (ENSG00000168267), MSC (ENSG00000178860), FIGLA (ENSG00000183733), BHLHA9 (ENSG00000205899), TWIST2 (ENSG00000233608), SCX (ENSG00000260428)

Protein

Protein identifiers

Transcription factor 24 — Q7RTU0 (reviewed: Q7RTU0)

All UniProt accessions (1): Q7RTU0

UniProt curated annotations — full annotation on UniProt →

Function. Putative transcription factor.

Subunit / interactions. Efficient DNA binding requires dimerization with another bHLH protein.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001180431* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011598	bHLH_dom	Domain
IPR036638	HLH_DNA-bd_sf	Homologous_superfamily
IPR050283	E-box_TF_Regulators	Family

Pfam: PF00010

UniProt features (6 total): compositionally biased region 3, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7RTU0-F1	68.14	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, chr8q13, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR23A_3P_MIR23B_3P, MIR23C, MIR548AW, MIR374A_5P, MIR141_3P, MIR200A_3P, MIR374B_5P, MIR519A_2_5P_MIR520B_5P, MIR4297, GSE10463_CD40L_AND_VA347_VS_CD40L_IN_DC_DN

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), developmental process (GO:0032502)

GO Molecular Function (5): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), protein dimerization activity (GO:0046983), DNA binding (GO:0003677), protein binding (GO:0005515)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
biological_process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
protein binding	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

262 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
TCF24	OLFML2A	Q68BL7	506
TCF24	ERICH2	A1L162	472
TCF24	ZNF24	P17028	436
TCF24	GRTP1	Q5TC63	400
TCF24	ASCL5	Q7RTU5	389
TCF24	ARHGAP42	A6NI28	375
TCF24	RNF144A	P50876	373
TCF24	MAD2L1BP	Q15013	373
TCF24	MIER2	Q8N344	363
TCF24	PPP1R42	Q7Z4L9	363
TCF24	ARHGAP32	A7KAX9	356
TCF24	MALSU1	Q96EH3	340
TCF24	PRDM9	Q9NQV7	323
TCF24	ANKRD9	Q96BM1	322
TCF24	ASCL4	Q6XD76	318

IntAct

9 interactions, top by confidence:

A	B	Type	Score
MAGEC3	TCF24	psi-mi:“MI:0915”(physical association)	0.560
TCF24	MAGEC3	psi-mi:“MI:0915”(physical association)	0.560
TCF4	TCF24	psi-mi:“MI:0915”(physical association)	0.560
TCF4	CBFA2T3	psi-mi:“MI:0914”(association)	0.530
TCF4	CBFA2T3	psi-mi:“MI:0914”(association)	0.350
TCF24	TCF4	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): TCF24 (Affinity Capture-MS), TCF24 (Affinity Capture-MS), TCF24 (Protein-RNA), TCF24 (Two-hybrid), TCF24 (Two-hybrid), TCF24 (Affinity Capture-MS), TCF24 (Affinity Capture-MS)

ESM2 similar proteins: A0A286YF58, A0A494C0N9, A0A494C0Y3, A0A7I2V3R4, A2VDX9, A5A769, A5PJP1, A6NIN4, A6NJG2, A6NLJ0, C9JTQ0, O14492, O15370, O35182, O43541, O88940, P0DPE3, P28283, P58267, Q12870, Q14681, Q29RM6, Q2KJ18, Q53LP3, Q60539, Q60756, Q64124, Q6F5E0, Q6QNY0, Q6XD76, Q7RTU0, Q7RTU7, Q80WY3, Q80XF7, Q86Y97, Q8BY98, Q8K025, Q8N912, Q8NCU7, Q8WY41

Diamond homologs: A8E5T6, B6VQA1, O13125, O13126, O16867, O35437, O42202, O42606, O43680, O57598, O60682, O73615, O73823, O88940, O93507, O96004, O96642, P13903, P17542, P22091, P24899, P26687, P46581, P48985, P48987, P57100, P57101, P57102, P59101, P61295, P61296, P70661, P79765, P79782, P97831, P97832, Q02575, Q02576, Q02577, Q0VCE2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

415 predictions. Top by Δscore:

Variant	Effect	Δscore
8:66948162:TTT:T	acceptor_gain	0.9900
8:66961370:GCTTA:G	donor_loss	0.9900
8:66961371:CTTA:C	donor_loss	0.9900
8:66961372:TTAC:T	donor_loss	0.9900
8:66961373:TAC:T	donor_loss	0.9900
8:66961375:C:CG	donor_loss	0.9900
8:66962332:T:A	donor_gain	0.9900
8:66948164:TC:T	acceptor_loss	0.9800
8:66948165:C:CG	acceptor_loss	0.9800
8:66948166:T:G	acceptor_loss	0.9800
8:66961377:TTG:T	donor_gain	0.9800
8:66948160:CATTT:C	acceptor_gain	0.9700
8:66948165:C:CC	acceptor_gain	0.9700
8:66948167:G:C	acceptor_loss	0.9700
8:66961276:C:T	acceptor_gain	0.9700
8:66948163:TT:T	acceptor_gain	0.9600
8:66957831:C:CT	donor_gain	0.9500
8:66957832:T:TT	donor_gain	0.9500
8:66961922:G:A	donor_gain	0.9400
8:66948168:AAAAA:A	acceptor_loss	0.9100
8:66961374:A:AC	donor_gain	0.9100
8:66961375:C:CC	donor_gain	0.9100
8:66961375:CCT:C	donor_gain	0.9000
8:66948175:T:TC	acceptor_gain	0.8900
8:66948362:CAG:C	acceptor_gain	0.8900
8:66948363:AGA:A	acceptor_gain	0.8900
8:66962321:CCCCT:C	donor_loss	0.8900
8:66962322:CCCTC:C	donor_loss	0.8900
8:66962323:CCTCA:C	donor_loss	0.8900
8:66962324:CTCA:C	donor_loss	0.8900

AlphaMissense

1043 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:66948159:C:A	W132C	1.000
8:66948159:C:G	W132C	1.000
8:66948161:A:G	W132R	1.000
8:66948161:A:T	W132R	1.000
8:66961464:A:G	L101P	1.000
8:66961473:A:T	I98N	1.000
8:66961505:C:A	K87N	1.000
8:66961505:C:G	K87N	1.000
8:66961507:T:C	K87E	1.000
8:66961551:A:G	L72P	1.000
8:66961559:G:C	F69L	1.000
8:66961559:G:T	F69L	1.000
8:66961561:A:G	F69L	1.000
8:66961477:A:C	Y97D	0.999
8:66961485:G:T	A94D	0.999
8:66961486:C:G	A94P	0.999
8:66961488:A:G	L93P	0.999
8:66961494:A:G	L91P	0.999
8:66961494:A:T	L91Q	0.999
8:66961500:T:A	D89V	0.999
8:66961503:A:G	L88P	0.999
8:66961506:T:A	K87M	0.999
8:66961507:T:G	K87Q	0.999
8:66961509:G:A	S86F	0.999
8:66961509:G:T	S86Y	0.999
8:66961551:A:T	L72Q	0.999
8:66961560:A:C	F69C	0.999
8:66961560:A:G	F69S	0.999
8:66961572:A:G	L65P	0.999
8:66961592:C:A	E58D	0.999

dbSNP variants (sampled 300 via entrez): RS1000100945 (8:66954040 A>T), RS1000552692 (8:66953680 C>G), RS1000577152 (8:66948542 T>C), RS1000952695 (8:66958058 A>C), RS1001178986 (8:66954984 C>T), RS1001447262 (8:66959818 C>T), RS1001497666 (8:66946479 G>A), RS1001555807 (8:66953604 G>C), RS1001608181 (8:66953192 G>A,T), RS1001616699 (8:66961276 C>G), RS1001923873 (8:66959370 A>G), RS1001953710 (8:66959821 T>C), RS1002025595 (8:66948939 A>C), RS1002110230 (8:66948258 G>A,T), RS1002174946 (8:66954869 G>A,T)

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
GCST007354_2	Intracranial aneurysm	3.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
entinostat	increases expression, affects cotreatment	2
triadimefon	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Arsenic Trioxide	decreases expression	1
Cadmium	increases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Tobacco Smoke Pollution	increases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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