PHF20

Summary

PHF20 (PHD finger protein 20, HGNC:16098) is a protein-coding gene on chromosome 20q11.22-q11.23, encoding PHD finger protein 20 (Q9BVI0). Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in cytosol; nuclear membrane; and nucleoplasm. Part of MLL1 complex and NSL complex.

Source: NCBI Gene 51230 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 136 total — 2 likely-pathogenic
• Druggable target: yes
• Transcription factor: yes — 12 downstream targets (CollecTRI)
• MANE Select transcript: NM_016436

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16098
Approved symbol	PHF20
Name	PHD finger protein 20
Location	20q11.22-q11.23
Locus type	gene with protein product
Status	Approved
Aliases	dJ1121G12.1, TDRD20A
Ensembl gene	ENSG00000025293
Ensembl biotype	protein_coding
OMIM	610335
Entrez	51230

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 13 protein_coding, 7 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000339089, ENST00000374000, ENST00000374012, ENST00000420233, ENST00000449988, ENST00000452270, ENST00000461122, ENST00000461405, ENST00000473943, ENST00000480940, ENST00000481202, ENST00000485604, ENST00000486408, ENST00000495338, ENST00000496305, ENST00000617560, ENST00000937485, ENST00000937486, ENST00000937487, ENST00000937488, ENST00000937489, ENST00000937490, ENST00000937491, ENST00000942256

RefSeq mRNA: 1 — MANE Select: NM_016436 NM_016436

CCDS: CCDS13268

Canonical transcript exons

ENST00000374012 — 18 exons

Exon	Start	End
ENSE00001708235	35947485	35950370
ENSE00001932718	35772015	35772079
ENSE00003465754	35938697	35939108
ENSE00003467323	35863013	35863400
ENSE00003471067	35871650	35871829
ENSE00003477874	35801491	35801605
ENSE00003488496	35917484	35917662
ENSE00003508936	35842573	35842744
ENSE00003530050	35899370	35899648
ENSE00003565145	35931249	35931444
ENSE00003591667	35927780	35927879
ENSE00003601379	35858302	35858381
ENSE00003611670	35847350	35847434
ENSE00003658168	35940864	35941047
ENSE00003670385	35870955	35871134
ENSE00003722422	35914033	35914197
ENSE00003736311	35913249	35913347
ENSE00003750286	35869438	35869551

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 97.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.8316 / max 1068.6663, expressed in 1825 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184328	48.0597	1825
184330	0.7339	166
184329	0.0380	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.87	gold quality
sperm	CL:0000019	97.36	gold quality
colonic epithelium	UBERON:0000397	96.67	gold quality
calcaneal tendon	UBERON:0003701	96.43	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.23	gold quality
germinal epithelium of ovary	UBERON:0001304	95.98	gold quality
amniotic fluid	UBERON:0000173	95.81	gold quality
gluteal muscle	UBERON:0002000	95.60	gold quality
visceral pleura	UBERON:0002401	95.60	gold quality
male germ cell	CL:0000015	95.50	gold quality
parietal pleura	UBERON:0002400	95.42	gold quality
pleura	UBERON:0000977	95.31	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.43	gold quality
monocyte	CL:0000576	94.41	gold quality
cortical plate	UBERON:0005343	94.22	gold quality
tonsil	UBERON:0002372	94.14	gold quality
mononuclear cell	CL:0000842	94.02	gold quality
leukocyte	CL:0000738	93.93	gold quality
gastrocnemius	UBERON:0001388	93.92	gold quality
synovial joint	UBERON:0002217	93.92	gold quality
middle temporal gyrus	UBERON:0002771	93.86	gold quality
biceps brachii	UBERON:0001507	93.63	gold quality
blood vessel layer	UBERON:0004797	93.62	gold quality
muscle of leg	UBERON:0001383	93.60	gold quality
saphenous vein	UBERON:0007318	93.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.48	gold quality
cauda epididymis	UBERON:0004360	93.45	gold quality
superficial temporal artery	UBERON:0001614	93.26	gold quality
choroid plexus epithelium	UBERON:0003911	93.21	gold quality
corpus callosum	UBERON:0002336	93.19	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	15.36

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

12 targets.

Target	Regulation
CDKN2A
CIITA
CYP11A1
ERVK-11
GH1
GPS2
HLA-E
KRAS
PGK1
POU1F1
TGFB1I1
TRU-TCA1-1

miRNA regulators (miRDB)

178 targeting PHF20, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-23B-5P	99.98	66.07	587
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-23A-5P	99.94	65.39	468
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-454-3P	99.91	74.01	1925

Literature-anchored findings (GeneRIF, showing 14)

• Survival of patients with GLEA2 antibodies was increased to 17.4 months and for patients with PHF3 antibodies to 14.7 months, as compared to 7.2 months for patients without GLEA2 or PHF3 antibodies in glioblastoma. (PMID:15906353)
• GLEA2 seroreactivity was increased by the time of surgery, decreased after surgery, increased again under radiation, and slightly decreased after radiation (PMID:18478111)
• genetic alterations of TSPAN14, SLC2A13 and PHF20 could play a role in non-small-cell lung cancer promotion (PMID:19473719)
• Data report the crystal structures of the N-terminal Tudor domains of PHF20 and highlight the novel structural features of each domain. (PMID:22449972)
• Association with PHF20 promotes stabilization and activation of p53 by diminishing Mdm2-mediated p53 ubiquitylation and degradation. (PMID:22864287)
• PHF20 is a novel substrate for PKB and its phosphorylation by PKB plays an important role in tumorigenesis via regulating of p53 mediated signaling. (PMID:22975685)
• Plant homeodomain finger protein 20 (PHF20) maintains NF-kappaB in an active state in the nucleus by inhibiting the interaction between PP2A and p65. (PMID:23797602)
• suggests a del(20q)-independent decrease in PHF20 expression in primary myelofibrosis (PMID:24675105)
• PHF20 may play an important role in Non-small-cell lung cancer (NSCLC). (PMID:26722404)
• Along with the PHF20/MOF complex, G9a links the crosstalk between ERalpha methylation and histone acetylation that governs the epigenetic regulation of hormonal gene expression. (PMID:26960573)
• These findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and dimethylated lysine 4 of histone H3, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin. (PMID:27760318)
• PHF20 interacts with poly(ADP-ribose) polymerase 1 (PARP1) and directly binds to promoter regions of octamer-binding transcription factor 4 (OCT4) and sex determining region Y-box 2 (SOX2) to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit (H3K4me3). (PMID:29452418)
• PHF20 inhibition promotes apoptosis and cisplatin chemosensitivity via the OCT4pSTAT3MCL1 signaling pathway in hypopharyngeal squamous cell carcinoma. (PMID:33982773)
• N6-methyladenosine demethylase ALKBH5 suppresses colorectal cancer progression potentially by decreasing PHF20 mRNA methylation. (PMID:35979628)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	phf20a	ENSDARG00000002750
danio_rerio	phf20b	ENSDARG00000038737
mus_musculus	Phf20	ENSMUSG00000038116
rattus_norvegicus	Phf20	ENSRNOG00000019948
drosophila_melanogaster	MBD-R2	FBGN0038016

Paralogs (1): PHF20L1 (ENSG00000129292)

Protein

Protein identifiers

PHD finger protein 20 — Q9BVI0 (reviewed: Q9BVI0)

Alternative names: Glioma-expressed antigen 2, Hepatocellular carcinoma-associated antigen 58, Novel zinc finger protein, Transcription factor TZP

All UniProt accessions (6): B0QYY0, B0QZ19, F8WCQ1, Q5JWZ0, Q5JXL1, Q9BVI0

UniProt curated annotations — full annotation on UniProt →

Function. Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. Not required for maintaining the global histone H4 ‘Lys-16’ acetylation (H4K16ac) levels or locus specific histone acetylation, but instead works downstream in transcriptional regulation of MOF target genes. As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. Contributes to methyllysine-dependent p53/TP53 stabilization and up-regulation after DNA damage.

Subunit / interactions. Homodimer; disulfide-linked. Component of some MLL1/MLL complex, at least composed of the core components KMT2A/MLL1, ASH2L, HCFC1, WDR5 and RBBP5, as well as the facultative components BACC1, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, KAT8/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Component of the NSL complex at least composed of MOF/KAT8, KANSL1, KANSL2, KANSL3, MCRS1, PHF20, OGT1/OGT, WDR5 and HCFC1.

Subcellular location. Nucleus.

Tissue specificity. Expressed in heart, kidney, liver, lung, pancreas, placenta, spleen and testis. Not expressed in brain, skeletal muscle, colon, ovary, prostate, small intestine and thymus. Expressed in colon and ovary cancer cell lines while it is not expressed in the respective normal tissues.

Post-translational modifications. Ubiquitinated by TRIM26; leading to proteasomal degradation.

Domain organisation. The Tudor domain 2 mediates reading of dimethyl-lysine residues. The Tudor domain 1 doesn’t bind dimethyl-lysine residues, due to an atypical and occluded aromatic cage.

Miscellaneous. Antibodies against PHF20 are present in sera from patients with hepatocellular carcinoma, glioblastoma and childhood medulloblastula.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BVI0-1	1	yes
Q9BVI0-2	2

RefSeq proteins (1): NP_057520* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR002999	Tudor	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR013087	Znf_C2H2_type	Domain
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR022255	PHF20_AT-hook	Domain
IPR041297	Crb2_Tudor	Domain
IPR043449	PHF20-like	Family

Pfam: PF12618, PF18115, PF20826

UniProt features (59 total): strand 13, compositionally biased region 8, sequence conflict 7, turn 6, modified residue 5, mutagenesis site 4, region of interest 3, domain 2, disulfide bond 2, splice variant 2, zinc finger region 2, helix 2, chain 1, sequence variant 1, DNA-binding region 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
5TAB	X-RAY DIFFRACTION	1.25
3SD4	X-RAY DIFFRACTION	1.93
3P8D	X-RAY DIFFRACTION	2
3QII	X-RAY DIFFRACTION	2.3
3Q1J	X-RAY DIFFRACTION	2.35
2LDM	SOLUTION NMR
5TBN	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BVI0-F1	55.32	0.18

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): 159, 488, 843, 878, 880

Disulfide bonds (2): 96, 100

Mutagenesis-validated functional residues (4):

Position	Phenotype
96	abolishes homodimerization.
97	abolishes interaction with methylated p53.
100	abolishes homodimerization.
103	abolishes interaction with methylated p53.

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-3214847	HATs acetylate histones
R-HSA-6804757	Regulation of TP53 Degradation
R-HSA-6804759	Regulation of TP53 Activity through Association with Co-factors
R-HSA-69541	Stabilization of p53
R-HSA-9772755	Formation of WDR5-containing histone-modifying complexes

MSigDB gene sets: 238 (showing top): BROWNE_HCMV_INFECTION_6HR_DN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON, AAGCCAT_MIR135A_MIR135B, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, SP1_Q2_01, NFKB_Q6, BROWNE_HCMV_INFECTION_48HR_DN, NFKB_C, CAGCAGG_MIR370, BLALOCK_ALZHEIMERS_DISEASE_UP, USF_01, E4F1_Q6, AACTTT_UNKNOWN, VDR_Q3

GO Biological Process (4): chromatin organization (GO:0006325), regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of DNA-templated transcription (GO:0045893), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): histone acetyltransferase complex (GO:0000123), nucleoplasm (GO:0005654), cytosol (GO:0005829), nuclear membrane (GO:0031965), NSL complex (GO:0044545), MLL1 complex (GO:0071339), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
Chromatin modifying enzymes	1
Regulation of TP53 Expression and Degradation	1
Regulation of TP53 Activity	1
p53-Dependent G1 DNA Damage Response	1
Epigenetic regulation by WDR5-containing histone modifying complexes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
DNA-templated transcription	2
cellular anatomical structure	2
cellular component organization	1
transcription by RNA polymerase II	1
positive regulation of RNA biosynthetic process	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
chromatin	1
protein acetyltransferase complex	1
nuclear lumen	1
cytoplasm	1
nucleus	1
nuclear envelope	1
organelle membrane	1
H4 histone acetyltransferase complex	1
MLL1/2 complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2324 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHF20	KANSL2	Q9H9L4	966
PHF20	KANSL3	Q9P2N6	960
PHF20	MCRS1	Q96EZ8	953
PHF20	KANSL1	Q7Z3B3	952
PHF20	NPLOC4	Q8TAT6	926
PHF20	WDR5	P61964	897
PHF20	TP53	P04637	871
PHF20	TAB3	Q8N5C8	799
PHF20	OGT	O15294	789
PHF20	TAB2	Q9NYJ8	781
PHF20	KAT8	Q9H7Z6	676
PHF20	RNF31	Q96EP0	669
PHF20	UBD	O15205	663
PHF20	MYT1L	Q9UL68	662
PHF20	ZNF629	Q9UEG4	638
PHF20	ZNF436	Q9C0F3	638

IntAct

30 interactions, top by confidence:

A	B	Type	Score
WDR5	MEN1	psi-mi:“MI:0914”(association)	0.710
PHF20	H3C1	psi-mi:“MI:0407”(direct interaction)	0.650
KANSL1	FOXK2	psi-mi:“MI:0914”(association)	0.640
PHF20	KANSL1	psi-mi:“MI:0914”(association)	0.640
PHF20	KANSL3	psi-mi:“MI:0915”(physical association)	0.620
PHF20	H4C16	psi-mi:“MI:0407”(direct interaction)	0.620
KANSL1	PHF20L1	psi-mi:“MI:0914”(association)	0.530
PHF20	PTPN14	psi-mi:“MI:0914”(association)	0.530
Kdm6b	PHF20	psi-mi:“MI:0915”(physical association)	0.490
PHF20	Kdm6b	psi-mi:“MI:0915”(physical association)	0.490
Dlg4	PHF20	psi-mi:“MI:0407”(direct interaction)	0.440
HNRNPA2B1	PHF20	psi-mi:“MI:0915”(physical association)	0.400
Kat8	PHF20L1	psi-mi:“MI:0915”(physical association)	0.400
Ube2k	ZFTRAF1	psi-mi:“MI:0914”(association)	0.350
TFG	NCOA4	psi-mi:“MI:0914”(association)	0.350
WDR5	PHF20L1	psi-mi:“MI:0914”(association)	0.350
MYC		psi-mi:“MI:0914”(association)	0.350
WDR5	TAF4	psi-mi:“MI:0914”(association)	0.350
KANSL3	POTEF	psi-mi:“MI:0914”(association)	0.350
SLC22A4	RTL8C	psi-mi:“MI:0914”(association)	0.350
KANSL1	ECI2	psi-mi:“MI:0914”(association)	0.350

BioGRID (63): PHF20 (Affinity Capture-RNA), PHF20 (Affinity Capture-RNA), POLE3 (Co-fractionation), PHF20 (Affinity Capture-MS), PHF20 (Affinity Capture-MS), PHF20 (Affinity Capture-MS), KANSL3 (Affinity Capture-MS), KANSL2 (Affinity Capture-MS), KAT8 (Affinity Capture-MS), MCRS1 (Affinity Capture-MS), PTPN14 (Affinity Capture-MS), PHF20 (Affinity Capture-RNA), PHF20 (Affinity Capture-MS), PHF20 (Affinity Capture-RNA), PHF20 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IYX6, A0A1L8H0H2, A5X7A0, A7XYJ6, E1BE02, F6NSX9, F8VPJ6, O35914, O57415, P37275, P59598, P59759, Q03172, Q13029, Q2KHR2, Q3UH06, Q5EXX3, Q5R7F2, Q5ZIE8, Q5ZLR2, Q62947, Q63755, Q64318, Q6NRM0, Q6ZPY7, Q76L83, Q7LBC6, Q7YR76, Q80VX4, Q86V15, Q8BHZ4, Q8BLG0, Q8BRH4, Q8BX22, Q8BZ32, Q8C0C0, Q8IZQ8, Q8NEZ4, Q8R5I7, Q8VIM5

Diamond homologs: A2VE56, A8MW92, Q4V9H5, Q5F3G6, Q8BLG0, Q8CCJ9, Q9BVI0, A5DDB7, Q1MTR4, Q6BNY5, Q6FJ00, Q7X6Y7, Q9VGA4, O44498, P36124, Q08923, Q10362, Q3UG20, Q6C0K9, Q8IZD2, Q99MY8, Q9NR48, Q9U263, Q9Y7V2, P42948, Q6IQX0, Q12830, Q9FEN9, Q9W0T1, Q9VW15, Q6L4L4, Q9FMS5, Q2LAE1, Q5XJV7, Q945S8, Q9C0A6, Q9M1X9, Q9VYD1, A5D962, O75151

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
AKT	down-regulates	PHF20	phosphorylation
AKT1	down-regulates	PHF20	phosphorylation
PHF20	“form complex”	“NSL histone acetyltransferase”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Formation of WDR5-containing histone-modifying complexes	5	83.0×	5e-07
Formation of the beta-catenin:TCF transactivating complex	5	37.6×	1e-05
HATs acetylate histones	5	24.8×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	2
Uncertain significance	102
Likely benign	2
Benign	8

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
599579	NM_016436.5(PHF20):c.2593G>A (p.Asp865Asn)	Likely pathogenic
599580	NM_016436.5(PHF20):c.890C>T (p.Pro297Leu)	Likely pathogenic

SpliceAI

3900 predictions. Top by Δscore:

Variant	Effect	Δscore
20:35800165:G:GT	donor_gain	1.0000
20:35800166:A:T	donor_gain	1.0000
20:35801603:CTGGT:C	donor_loss	1.0000
20:35801606:G:A	donor_loss	1.0000
20:35801607:T:A	donor_loss	1.0000
20:35842565:T:TA	acceptor_gain	1.0000
20:35842741:TTCT:T	donor_gain	1.0000
20:35842742:TCT:T	donor_gain	1.0000
20:35842742:TCTGT:T	donor_loss	1.0000
20:35842745:G:GG	donor_gain	1.0000
20:35842745:GTGAG:G	donor_loss	1.0000
20:35842746:T:G	donor_loss	1.0000
20:35842749:G:C	donor_loss	1.0000
20:35842749:G:GG	donor_gain	1.0000
20:35847430:GGATG:G	donor_gain	1.0000
20:35847431:GATGG:G	donor_gain	1.0000
20:35847440:GCATT:G	donor_gain	1.0000
20:35869416:T:TA	acceptor_gain	1.0000
20:35869418:T:TA	acceptor_gain	1.0000
20:35869419:G:A	acceptor_gain	1.0000
20:35869425:A:AG	acceptor_gain	1.0000
20:35869426:T:G	acceptor_gain	1.0000
20:35869427:A:AG	acceptor_gain	1.0000
20:35869431:AT:A	acceptor_gain	1.0000
20:35870953:A:AG	acceptor_gain	1.0000
20:35870954:G:GG	acceptor_gain	1.0000
20:35871131:GAAG:G	donor_gain	1.0000
20:35871132:AAGGT:A	donor_loss	1.0000
20:35871133:AGGT:A	donor_loss	1.0000
20:35871134:GGT:G	donor_loss	1.0000

AlphaMissense

6697 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:35801559:T:C	F13L	1.000
20:35801560:T:C	F13S	1.000
20:35801560:T:G	F13C	1.000
20:35801561:T:A	F13L	1.000
20:35801561:T:G	F13L	1.000
20:35801578:T:C	L19S	1.000
20:35801604:T:A	W28R	1.000
20:35801604:T:C	W28R	1.000
20:35842573:G:C	W28C	1.000
20:35842573:G:T	W28C	1.000
20:35842574:T:G	Y29D	1.000
20:35842581:C:A	A31D	1.000
20:35842587:T:A	I33K	1.000
20:35842587:T:G	I33R	1.000
20:35842620:T:C	L44P	1.000
20:35842623:T:A	I45N	1.000
20:35842623:T:C	I45T	1.000
20:35842623:T:G	I45S	1.000
20:35842625:C:G	H46D	1.000
20:35842628:T:A	F47I	1.000
20:35842628:T:C	F47L	1.000
20:35842628:T:G	F47V	1.000
20:35842629:T:C	F47S	1.000
20:35842629:T:G	F47C	1.000
20:35842630:C:A	F47L	1.000
20:35842630:C:G	F47L	1.000
20:35842637:T:A	W50R	1.000
20:35842637:T:C	W50R	1.000
20:35842638:G:C	W50S	1.000
20:35842639:G:C	W50C	1.000

dbSNP variants (sampled 300 via entrez): RS1000047511 (20:35936654 G>T), RS1000053582 (20:35939365 G>A,T), RS1000063960 (20:35881596 A>ACATT), RS1000079151 (20:35874742 A>C), RS1000088540 (20:35783426 T>TTTTC), RS1000094511 (20:35811651 G>T), RS1000106386 (20:35832840 G>A), RS1000118909 (20:35880872 A>G), RS1000150960 (20:35929067 C>A), RS1000151975 (20:35855959 G>A), RS1000214648 (20:35875040 C>G), RS1000221445 (20:35943253 C>T), RS1000226086 (20:35845856 C>T), RS1000256548 (20:35841953 A>G,T), RS1000259920 (20:35881088 G>A)

Disease associations

OMIM: gene MIM:610335 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST002647_170	Height	3.000000e-52
GCST006269_694	General cognitive ability	1.000000e-09
GCST008163_629	Height	9.000000e-06
GCST010002_66	Refractive error	2.000000e-20
GCST012227_1147	Hip circumference adjusted for BMI	3.000000e-10
GCST012227_1148	Hip circumference adjusted for BMI	3.000000e-09
GCST90002395_595	Mean platelet volume	9.000000e-12
GCST90020028_1562	Hip circumference adjusted for BMI	7.000000e-14
GCST90020029_193	Waist circumference adjusted for body mass index	1.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067596 (SINGLE PROTEIN)

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.25	Kd	5600	nM	CHEMBL2426364

PubChem BioAssay actives

1 with measured affinity, of 1 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
[3-anilino-4-(4-pyrrolidin-1-ylpiperidine-1-carbonyl)phenyl]-(4-pyrrolidin-1-ylpiperidin-1-yl)methanone	2189761: Binding affinity to PHF20 (unknown origin) by ITC assay	kd	5.6000	uM

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	2
Benzo(a)pyrene	increases methylation, affects methylation, decreases expression	2
FR900359	affects phosphorylation	1
TAK-243	increases sumoylation	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	affects methylation	1
cobaltous chloride	increases expression	1
benzo(e)pyrene	increases methylation	1
CGP 52608	affects binding, increases reaction	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	increases methylation	1
Arsenic	increases methylation	1
Atrazine	increases expression	1
Vehicle Emissions	increases abundance, decreases expression	1
Lead	decreases expression	1
Methapyrilene	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thimerosal	increases expression	1
Valproic Acid	decreases expression	1
Vitamin E	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Copper Sulfate	increases expression	1
Chlorodiphenyl (54% Chlorine)	increases expression	1
Particulate Matter	increases abundance, decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5712136	Binding	Binding affinity to PHF20 (unknown origin) by ITC assay	Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. — Nat Chem Biol

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D9MP	Ubigene HEK293 PHF20 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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