PHF24

Summary

PHF24 (PHD finger protein 24, HGNC:29180) is a protein-coding gene on chromosome 9p13.3, encoding PHD finger protein 24 (Q9UPV7).

Predicted to enable transcription corepressor activity. Predicted to be involved in negative regulation of DNA-templated transcription. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. Predicted to be active in glutamatergic synapse; nucleus; and synaptic vesicle membrane.

Source: NCBI Gene 23349 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 277 total
• MANE Select transcript: NM_015297

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29180
Approved symbol	PHF24
Name	PHD finger protein 24
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Aliases	GINIP
Ensembl gene	ENSG00000122733
Ensembl biotype	protein_coding
OMIM	619928
Entrez	23349

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000242315, ENST00000440503, ENST00000476115, ENST00000486477, ENST00000948628

RefSeq mRNA: 8 — MANE Select: NM_015297 NM_001304333, NM_001347982, NM_001347983, NM_001395369, NM_001395370, NM_001395371, NM_001395372, NM_015297

CCDS: CCDS43796

Canonical transcript exons

ENST00000242315 — 8 exons

Exon	Start	End
ENSE00000697637	34971295	34971676
ENSE00000832961	34972346	34972531
ENSE00000832966	34978015	34982544
ENSE00003515536	34977546	34977641
ENSE00003600589	34976535	34976740
ENSE00003609571	34977083	34977243
ENSE00003624114	34976152	34976230
ENSE00003978142	34958285	34958401

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 94.70.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9375 / max 129.2000, expressed in 201 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96548	0.6667	98
96537	0.3251	78
96539	0.1695	76
96547	0.1648	60
96541	0.1120	51
96538	0.0992	46
96544	0.0771	44
96546	0.0621	37
96540	0.0601	35
96535	0.0566	28

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	94.70	gold quality
middle temporal gyrus	UBERON:0002771	94.09	gold quality
right frontal lobe	UBERON:0002810	93.45	gold quality
frontal cortex	UBERON:0001870	93.01	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	92.90	gold quality
frontal pole	UBERON:0002795	92.66	gold quality
orbitofrontal cortex	UBERON:0004167	92.66	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.37	gold quality
neocortex	UBERON:0001950	92.27	gold quality
cingulate cortex	UBERON:0003027	92.15	gold quality
anterior cingulate cortex	UBERON:0009835	92.08	gold quality
primary visual cortex	UBERON:0002436	91.59	gold quality
superior frontal gyrus	UBERON:0002661	91.54	gold quality
Brodmann (1909) area 46	UBERON:0006483	91.35	gold quality
Brodmann (1909) area 10	UBERON:0013541	90.99	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.93	gold quality
cerebral cortex	UBERON:0000956	90.81	gold quality
occipital lobe	UBERON:0002021	89.46	gold quality
postcentral gyrus	UBERON:0002581	89.03	gold quality
entorhinal cortex	UBERON:0002728	88.78	gold quality
parietal lobe	UBERON:0001872	88.56	gold quality
CA1 field of hippocampus	UBERON:0003881	88.36	gold quality
telencephalon	UBERON:0001893	88.15	gold quality
temporal lobe	UBERON:0001871	87.88	gold quality
amygdala	UBERON:0001876	87.15	gold quality
cortical plate	UBERON:0005343	85.80	gold quality
paraflocculus	UBERON:0005351	85.28	gold quality
Ammon’s horn	UBERON:0001954	85.18	gold quality
nucleus accumbens	UBERON:0001882	84.99	gold quality
middle frontal gyrus	UBERON:0002702	84.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

253 targeting PHF24, 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-5196-5P	100.00	67.98	2761
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
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-7111-5P	99.97	68.48	2062
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-218-5P	99.93	72.22	2103

Literature-anchored findings (GeneRIF, showing 1)

• Cross-brace structural motifs are required as a scaffold to design artificial RING fingers (ARFs) that function as ubiquitin ligase (E3) in ubiquitination and have specific ubiquitin-conjugating enzyme (E2)-binding capabilities. (PMID:29430827)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	phf24	ENSDARG00000077596
mus_musculus	Phf24	ENSMUSG00000036062
rattus_norvegicus	Phf24	ENSRNOG00000000129
drosophila_melanogaster	TpnC47D	FBGN0010423
drosophila_melanogaster	TpnC73F	FBGN0010424
drosophila_melanogaster	TpnC41C	FBGN0013348

Paralogs (5): CAPS (ENSG00000105519), CAPSL (ENSG00000152611), CAPS2 (ENSG00000180881), EFCAB6 (ENSG00000186976), SPATA21 (ENSG00000187144)

Protein

Protein identifiers

PHD finger protein 24 — Q9UPV7 (reviewed: Q9UPV7)

All UniProt accessions (1): Q9UPV7

RefSeq proteins (8): NP_001291262, NP_001334911, NP_001334912, NP_001382298, NP_001382299, NP_001382300, NP_001382301, NP_056112* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR031946	KIAA1045_Zf_RING	Domain

Pfam: PF16744

UniProt features (17 total): modified residue 4, strand 3, turn 2, compositionally biased region 2, initiator methionine 1, chain 1, lipid moiety-binding region 1, helix 1, zinc finger region 1, region of interest 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
1WIL	SOLUTION NMR
5XHT	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UPV7-F1	74.20	0.41

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 (5): 2, 36, 43, 47, 51

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_DETECTION_OF_MECHANICAL_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION, GOBP_GAMMA_AMINOBUTYRIC_ACID_SIGNALING_PATHWAY, GOBP_CELL_CELL_SIGNALING, GOBP_DETECTION_OF_MECHANICAL_STIMULUS, GOBP_SENSORY_PERCEPTION_OF_PAIN, chr9p13, GOBP_SYNAPTIC_SIGNALING, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, GOBP_REGULATION_OF_SYNAPTIC_TRANSMISSION_GABAERGIC, MODULE_207, GOBP_RESPONSE_TO_MECHANICAL_STIMULUS

GO Biological Process (5): gamma-aminobutyric acid signaling pathway (GO:0007214), regulation of G protein-coupled receptor signaling pathway (GO:0008277), regulation of synaptic transmission, GABAergic (GO:0032228), detection of mechanical stimulus involved in sensory perception of pain (GO:0050966), negative regulation of DNA-templated transcription (GO:0045892)

GO Molecular Function (4): transcription corepressor activity (GO:0003714), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), synaptic vesicle membrane (GO:0030672), glutamatergic synapse (GO:0098978)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-cell signaling	1
GABA receptor activity	1
G protein-coupled receptor signaling pathway	1
regulation of signal transduction	1
modulation of chemical synaptic transmission	1
synaptic transmission, GABAergic	1
sensory perception of pain	1
detection of mechanical stimulus involved in sensory perception	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
negative regulation of RNA biosynthetic process	1
transcription coregulator activity	1
negative regulation of DNA-templated transcription	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
synaptic vesicle	1
exocytic vesicle membrane	1
synapse	1

Protein interactions and networks

STRING

212 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHF24	PCYOX1	Q9UHG3	470
PHF24	ASCL4	Q6XD76	461
PHF24	GABBR1	Q9UBS5	459
PHF24	LANCL1	O43813	457
PHF24	DYNC1I1	O14576	444
PHF24	FAM184B	Q9ULE4	444
PHF24	DENND2B	P78523	428
PHF24	CNTNAP3B	Q96NU0	419
PHF24	PIP4K2B	P78356	406
PHF24	PIRT	P0C851	401
PHF24	PHF21B	Q96EK2	379
PHF24	CA13	Q8N1Q1	374
PHF24	RAB6B	Q9NRW1	340
PHF24	TXNDC5	Q8NBS9	331
PHF24	CNTNAP3	Q9BZ76	328

IntAct

17 interactions, top by confidence:

A	B	Type	Score
PHF24	ZNF552	psi-mi:“MI:0915”(physical association)	0.560
THBD	PHF24	psi-mi:“MI:0915”(physical association)	0.560
PFDN5	PHF24	psi-mi:“MI:0915”(physical association)	0.560
ZNF552	PHF24	psi-mi:“MI:0915”(physical association)	0.560
GNAI3	PHF24	psi-mi:“MI:0915”(physical association)	0.560
TRIM35	PHF24	psi-mi:“MI:0915”(physical association)	0.560
PHF24	PPP1R18	psi-mi:“MI:0915”(physical association)	0.400
PHF24	THBD	psi-mi:“MI:0915”(physical association)	0.000
PHF24	PFDN5	psi-mi:“MI:0915”(physical association)	0.000
PHF24	TRIM35	psi-mi:“MI:0915”(physical association)	0.000
GNAI3	PHF24	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): KIAA1045 (Two-hybrid), KIAA1045 (Two-hybrid), PFDN5 (Two-hybrid), THBD (Two-hybrid), ZNF552 (Two-hybrid), KIAA1045 (Proximity Label-MS), KIAA1045 (Positive Genetic)

ESM2 similar proteins: A0A059XKS9, A0A125YS36, A0A125YYR0, A0A7J6K144, A0A7J6K7I9, A0A7J6K7Y0, A4HK17, A4I7K1, B5APK2, B9Q0C2, E9PSU6, F2YGR7, F4IVL6, F6N7K6, O04064, O48767, P0CH66, P23915, P24686, Q2PAY2, Q2PAY3, Q384Y0, Q387Y5, Q388F1, Q40504, Q40505, Q4CTY5, Q4D7L5, Q4DHA1, Q4Q5P8, Q57XK8, Q57XV5, Q580X6, Q5R4R7, Q6B9Y8, Q6GV23, Q75CM4, Q80TL4, Q84VW5, Q8L5Y5

Diamond homologs: Q5R4R7, Q80TL4, Q9UPV7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	242
Likely benign	24
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

1429 predictions. Top by Δscore:

Variant	Effect	Δscore
9:34965507:A:T	donor_gain	1.0000
9:34971290:CACA:C	acceptor_loss	1.0000
9:34971291:ACAG:A	acceptor_loss	1.0000
9:34971293:A:AG	acceptor_gain	1.0000
9:34971294:G:GG	acceptor_gain	1.0000
9:34971294:G:GT	acceptor_loss	1.0000
9:34971294:GA:G	acceptor_gain	1.0000
9:34971294:GAGCC:G	acceptor_gain	1.0000
9:34971673:GCCT:G	donor_gain	1.0000
9:34971677:G:GG	donor_gain	1.0000
9:34972528:CTGT:C	donor_gain	1.0000
9:34972530:GT:G	donor_gain	1.0000
9:34972531:TGTAA:T	donor_loss	1.0000
9:34972532:G:GG	donor_gain	1.0000
9:34972532:GTAA:G	donor_loss	1.0000
9:34972533:T:A	donor_loss	1.0000
9:34972534:AA:A	donor_loss	1.0000
9:34976147:TTCAG:T	acceptor_loss	1.0000
9:34976148:TCAGG:T	acceptor_loss	1.0000
9:34976149:CAGGA:C	acceptor_loss	1.0000
9:34976150:A:AG	acceptor_gain	1.0000
9:34976150:AG:A	acceptor_gain	1.0000
9:34976151:G:GC	acceptor_loss	1.0000
9:34976151:G:GT	acceptor_gain	1.0000
9:34976151:GG:G	acceptor_gain	1.0000
9:34976151:GGAC:G	acceptor_gain	1.0000
9:34976151:GGACA:G	acceptor_gain	1.0000
9:34976211:GCGGT:G	donor_gain	1.0000
9:34976215:TGTA:T	donor_gain	1.0000
9:34976216:GTAA:G	donor_gain	1.0000

AlphaMissense

2622 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:34971369:T:C	F24S	0.998
9:34972364:T:C	C133R	0.998
9:34972373:T:A	C136S	0.998
9:34972373:T:C	C136R	0.998
9:34972374:G:A	C136Y	0.998
9:34972374:G:C	C136S	0.998
9:34971368:T:C	F24L	0.997
9:34971370:C:A	F24L	0.997
9:34971370:C:G	F24L	0.997
9:34972364:T:A	C133S	0.997
9:34972365:G:A	C133Y	0.997
9:34972365:G:C	C133S	0.997
9:34972430:C:G	H155D	0.997
9:34972439:T:C	C158R	0.997
9:34971357:C:A	A20D	0.996
9:34972366:T:G	C133W	0.996
9:34972374:G:T	C136F	0.996
9:34972375:T:G	C136W	0.996
9:34972406:T:C	C147R	0.996
9:34972415:T:C	C150R	0.996
9:34972514:T:A	W183R	0.996
9:34972514:T:C	W183R	0.996
9:34972517:A:C	S184R	0.996
9:34972519:C:A	S184R	0.996
9:34972519:C:G	S184R	0.996
9:34972520:T:C	C185R	0.996
9:34976684:T:A	W265R	0.996
9:34976684:T:C	W265R	0.996
9:34976694:T:C	F268S	0.996
9:34971369:T:G	F24C	0.995

dbSNP variants (sampled 300 via entrez): RS1000009680 (9:34905329 G>A,T), RS1000023778 (9:34842864 C>T), RS1000029920 (9:34895036 T>C,G), RS1000041008 (9:34683434 A>C,G), RS1000044212 (9:34937024 G>A,C,T), RS1000050280 (9:34769290 A>G), RS1000059865 (9:34733460 G>A), RS1000070746 (9:34805950 T>A,C), RS1000079999 (9:34889249 A>G), RS1000091972 (9:34733129 C>A,G,T), RS1000107878 (9:34684990 G>T), RS1000114533 (9:34957007 C>T), RS1000118946 (9:34739866 T>A), RS1000133452 (9:34848784 G>C), RS1000161288 (9:34916699 T>C)

Disease associations

OMIM: gene MIM:619928 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): breast ductal adenocarcinoma (MONDO:0005590)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D018270	Carcinoma, Ductal, Breast	C04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, increases methylation	2
aristolochic acid I	increases expression	1
sodium arsenite	increases expression	1
ferrous chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Hydralazine	affects cotreatment, increases expression	1
Lead	affects expression	1
Lipopolysaccharides	increases expression, affects response to substance	1
Niclosamide	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	increases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Triclosan	decreases expression	1
Gold Compounds	increases expression	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03414970	PHASE3	ACTIVE_NOT_RECRUITING	Hypofractionated Radiation Therapy After Mastectomy in Preventing Recurrence in Patients With Stage IIa-IIIa Breast Cancer
NCT00461344	PHASE2	TERMINATED	Docetaxel + Doxorubicin as Neoadjuvant Chemotherapy in Patients With Breast Cancer
NCT07499999	PHASE2	NOT_YET_RECRUITING	Randomized Double-Blind Phase II Trial of Baby Exemestane Versus Baby Tamoxifen in Post-Menopausal Women at High Risk for Breast Cancer
NCT00637364	PHASE1/PHASE2	SUSPENDED	High Intensity Focused Ultrasound Tumor Treatment for Pancreatic Cancer Pain
NCT02779855	PHASE1/PHASE2	COMPLETED	Talimogene Laherparepvec in Combination With Neoadjuvant Chemotherapy in Triple Negative Breast Cancer
NCT01753908	EARLY_PHASE1	COMPLETED	Broccoli Sprout Extract in Treating Patients With Breast Cancer
NCT01796041	EARLY_PHASE1	COMPLETED	Intraoperative Imaging of Breast Cancer With Indocyanine Green
NCT01208974	Not specified	ACTIVE_NOT_RECRUITING	Nipple-Areola Complex (NAC) Irradiation After Nipple-Sparing Mastectomy and Reconstruction
NCT01875198	Not specified	TERMINATED	Oncologic Impact of Splenectomy-omitting Radical Pancreatectomy in Well-selected Left-sided Pancreatic Cancer
NCT03543397	Not specified	UNKNOWN	MRI in Ductal Carcinoma in Situ (DCIS)
NCT03834532	Not specified	COMPLETED	Living Well After Breast Surgery