PHF20L1

Summary

PHF20L1 (PHD finger protein 20 like 1, HGNC:24280) is a protein-coding gene on chromosome 8q24.22, encoding PHD finger protein 20-like protein 1 (A8MW92). Is a negative regulator of proteasomal degradation of a set of methylated proteins, including DNMT1 and SOX2.

Enables methylation-dependent protein binding activity. Involved in negative regulation of proteasomal ubiquitin-dependent protein catabolic process. Predicted to be located in nucleoplasm. Predicted to be part of NSL complex.

Source: NCBI Gene 51105 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 120 total
• Druggable target: yes
• MANE Select transcript: NM_016018

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24280
Approved symbol	PHF20L1
Name	PHD finger protein 20 like 1
Location	8q24.22
Locus type	gene with protein product
Status	Approved
Aliases	CGI-72, FLJ13649, MGC64923, FLJ21615, TDRD20B
Ensembl gene	ENSG00000129292
Ensembl biotype	protein_coding
OMIM	620050
Entrez	51105

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 23 protein_coding, 8 retained_intron, 3 nonsense_mediated_decay

ENST00000220847, ENST00000315808, ENST00000337920, ENST00000361997, ENST00000395374, ENST00000395376, ENST00000395379, ENST00000395383, ENST00000395386, ENST00000395390, ENST00000460236, ENST00000469979, ENST00000477051, ENST00000485595, ENST00000486199, ENST00000493126, ENST00000521038, ENST00000522253, ENST00000522580, ENST00000622263, ENST00000905698, ENST00000905699, ENST00000905700, ENST00000939785, ENST00000939786, ENST00000939787, ENST00000939788, ENST00000939789, ENST00000939790, ENST00000939791, ENST00000972149, ENST00000972150, ENST00000972151, ENST00000972152

RefSeq mRNA: 4 — MANE Select: NM_016018 NM_001277196, NM_001362971, NM_016018, NM_198513

CCDS: CCDS6367, CCDS6368, CCDS75791

Canonical transcript exons

ENST00000395386 — 21 exons

Exon	Start	End
ENSE00001521553	132775388	132775645
ENSE00001719560	132845781	132848807
ENSE00003484034	132836540	132836721
ENSE00003489307	132839387	132839582
ENSE00003535211	132844156	132844318
ENSE00003546412	132825264	132825371
ENSE00003620381	132842515	132842875
ENSE00003650249	132837712	132837811
ENSE00003702479	132794733	132794817
ENSE00003704031	132824004	132824060
ENSE00003704340	132794410	132794581
ENSE00003704840	132817339	132817545
ENSE00003705926	132798772	132798860
ENSE00003707614	132804615	132804740
ENSE00003707827	132777792	132777911
ENSE00003709579	132799095	132799172
ENSE00003709990	132811046	132811128
ENSE00003710191	132814637	132814889
ENSE00003710987	132803819	132804032
ENSE00003711118	132816888	132817076
ENSE00003728236	132832235	132832399

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 96.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 29.0187 / max 1517.2306, expressed in 1814 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
90830	27.7085	1810
90829	1.0444	643
90831	0.2174	82
90835	0.0485	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	96.51	gold quality
calcaneal tendon	UBERON:0003701	96.15	gold quality
cortical plate	UBERON:0005343	96.01	gold quality
ganglionic eminence	UBERON:0004023	95.97	gold quality
monocyte	CL:0000576	94.22	gold quality
sural nerve	UBERON:0015488	94.15	gold quality
mononuclear cell	CL:0000842	93.98	gold quality
sperm	CL:0000019	93.52	gold quality
leukocyte	CL:0000738	93.50	gold quality
left lobe of thyroid gland	UBERON:0001120	91.89	gold quality
ventricular zone	UBERON:0003053	91.86	gold quality
thyroid gland	UBERON:0002046	91.25	gold quality
right lobe of thyroid gland	UBERON:0001119	91.17	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.98	gold quality
male germ cell	CL:0000015	90.84	gold quality
bone marrow	UBERON:0002371	90.77	gold quality
blood	UBERON:0000178	90.73	gold quality
colonic epithelium	UBERON:0000397	90.65	gold quality
bone marrow cell	CL:0002092	90.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.29	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.05	gold quality
left ovary	UBERON:0002119	88.91	gold quality
secondary oocyte	CL:0000655	88.78	gold quality
adrenal gland	UBERON:0002369	88.72	gold quality
prefrontal cortex	UBERON:0000451	88.56	gold quality
adrenal cortex	UBERON:0001235	88.54	gold quality
cerebellar hemisphere	UBERON:0002245	88.50	gold quality
cerebellar cortex	UBERON:0002129	88.46	gold quality
left adrenal gland cortex	UBERON:0035825	88.35	gold quality
right adrenal gland cortex	UBERON:0035827	88.34	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.16
E-MTAB-7606	no	575.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

218 targeting PHF20L1, 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-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4482-3P	99.98	72.50	3147

Literature-anchored findings (GeneRIF, showing 9)

• Malignant brain tumor domain of PHF20L1 reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. (PMID:24492612)
• results demonstrated the oncogenic potential of PHF20L1 and its association with poor prognostic parameters in breast cancer. (PMID:26588862)
• Authors find that the interplay between PHF20L1 and mono-methyl pRb is important for maintaining the integrity of a pRb-dependent G1-S-phase checkpoint. Results highlight the distinct roles that methyl-lysine readers have in regulating the biological activity of pRb. (PMID:28841214)
• Data suggest that, in human ovarian teratocarcinoma cell line, methylation-dependent proteolysis of SOX2 is controlled by LSD1 and PHF20L1 via regulation of SET7 activity; these data are consistent with previous studies in mouse primary stem cells. (SOX2 = SRY-box 2 transcription factor; LSD1 = lysine demethylase-1A; PHF20L1 = PHD finger protein 20 like-1; SET7 = histone-lysine N-methyltransferase SETD7) (PMID:29358331)
• associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by the MLL1/WDR5 complexes (PMID:30089852)
• PHF20L1 as a H3K27me2 reader coordinates with transcriptional repressors to promote breast tumorigenesis. (PMID:32494608)
• An insight into the promoter methylation of PHF20L1 and the gene association with metastasis in breast cancer. (PMID:33847474)
• PHF20L1 mediates PAX2 expression to promote angiogenesis and liver metastasis in colorectal cancer through regulating HIC1. (PMID:35357096)
• Single-genome analysis reveals a heterogeneous association of the herpes simplex virus genome with H3K27me2 and the reader PHF20L1 following infection of human fibroblasts. (PMID:38411116)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	phf20l1	ENSDARG00000017427
mus_musculus	Phf20l1	ENSMUSG00000072501
rattus_norvegicus	Phf20l1	ENSRNOG00000005486
drosophila_melanogaster	MBD-R2	FBGN0038016

Paralogs (1): PHF20 (ENSG00000025293)

Protein

Protein identifiers

PHD finger protein 20-like protein 1 — A8MW92 (reviewed: A8MW92)

All UniProt accessions (10): A8MW92, A0A0A0MQS0, A0A0D9SG14, A8MUE8, A8MXR8, E5RK91, E9PM57, F8W9L8, H0YC05, H0YDF7

UniProt curated annotations — full annotation on UniProt →

Function. Is a negative regulator of proteasomal degradation of a set of methylated proteins, including DNMT1 and SOX2. Involved in the maintainance of embryonic stem cells pluripotency, through the regulation of SOX2 levels.

Subunit / interactions. Interacts with methylated DNMT1 (DNMT1K142me1). Interacts with SOX2.

Subcellular location. Nucleus.

Isoforms (3)

UniProt ID	Names	Canonical?
A8MW92-1	1	yes
A8MW92-2	2
A8MW92-4	4

RefSeq proteins (4): NP_001264125, NP_001349900, NP_057102, NP_940915 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002999	Tudor	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR014002	Agenet_dom_plant	Domain
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR040477	KDM4-like_Tudor	Domain
IPR043449	PHF20-like	Family
IPR047405	Tudor_PHF20L1	Domain

Pfam: PF16660, PF18104, PF20826

UniProt features (47 total): compositionally biased region 11, strand 9, splice variant 5, region of interest 5, cross-link 4, modified residue 3, turn 3, helix 3, domain 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

9 structures.

PDB	Method	Resolution (Å)
6L1P	X-RAY DIFFRACTION	1.23
6L0X	X-RAY DIFFRACTION	1.3
6L1C	X-RAY DIFFRACTION	1.58
6L10	X-RAY DIFFRACTION	1.6
6L1I	X-RAY DIFFRACTION	1.85
6L1F	X-RAY DIFFRACTION	1.9
2EQM	SOLUTION NMR
2EQU	SOLUTION NMR
2JTF	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MW92-F1	54.63	0.12

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 (7): 368, 433, 909, 75, 79, 530, 851

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9772755	Formation of WDR5-containing histone-modifying complexes

MSigDB gene sets: 290 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE18804_SPLEEN_MACROPHAGE_VS_BRAIN_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GSE45365_NK_CELL_VS_CD8A_DC_DN, GCACCTT_MIR18A_MIR18B, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, PAX4_01, LU_IL4_SIGNALING, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, SHEPARD_BMYB_MORPHOLINO_DN, ATGTTAA_MIR302C

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435), negative regulation of protein catabolic process (GO:0042177), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (4): zinc ion binding (GO:0008270), methylation-dependent protein binding (GO:0140034), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): nucleoplasm (GO:0005654), NSL complex (GO:0044545), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
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	1
transcription by RNA polymerase II	1
regulation of proteasomal ubiquitin-dependent protein catabolic process	1
proteasome-mediated ubiquitin-dependent protein catabolic process	1
negative regulation of proteasomal protein catabolic process	1
negative regulation of ubiquitin-dependent protein catabolic process	1
negative regulation of catabolic process	1
protein catabolic process	1
regulation of protein catabolic process	1
negative regulation of protein metabolic process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transition metal ion binding	1
modification-dependent protein binding	1
binding	1
cation binding	1
nuclear lumen	1
cellular anatomical structure	1
H4 histone acetyltransferase complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PHF20L1	L3MBTL3	Q96JM7	511
PHF20L1	ZNF280D	Q6N043	467
PHF20L1	ZNF512B	Q96KM6	465
PHF20L1	ANKMY2	Q8IV38	444
PHF20L1	HMG20A	Q9NP66	428
PHF20L1	TDRD10	Q5VZ19	419
PHF20L1	TSPAN13	O95857	416
PHF20L1	BAHD1	Q8TBE0	413
PHF20L1	PPP2R5C	Q13362	397
PHF20L1	LMAN2L	Q9H0V9	395
PHF20L1	SLC8B1	Q6J4K2	394
PHF20L1	NMT1	P30419	389
PHF20L1	CALHM6	Q5R3K3	382
PHF20L1	USP25	Q9UHP3	370
PHF20L1	L3MBTL1	Q9Y468	370

IntAct

23 interactions, top by confidence:

A	B	Type	Score
PHF20L1	H3C1	psi-mi:“MI:0407”(direct interaction)	0.560
PHF20L1	H4C16	psi-mi:“MI:0407”(direct interaction)	0.560
H4C16	PHF20L1	psi-mi:“MI:0407”(direct interaction)	0.560
KANSL1	PHF20L1	psi-mi:“MI:0914”(association)	0.530
Kat8	PHF20L1	psi-mi:“MI:0915”(physical association)	0.400
DNMT1	PHF20L1	psi-mi:“MI:0915”(physical association)	0.400
SNAP23	PHF20L1	psi-mi:“MI:0915”(physical association)	0.370
PHF20L1	CASP10	psi-mi:“MI:0915”(physical association)	0.370
ELAVL4	PHF20L1	psi-mi:“MI:0915”(physical association)	0.370
PHF20L1	WWP1	psi-mi:“MI:0915”(physical association)	0.370
PHF20L1	LYAR	psi-mi:“MI:0915”(physical association)	0.370
KDM1A	PHF20L1	psi-mi:“MI:0915”(physical association)	0.370
PB2	SEC15L3	psi-mi:“MI:0914”(association)	0.350
PB2		psi-mi:“MI:0914”(association)	0.350
PHF20L1	MTA2	psi-mi:“MI:0914”(association)	0.350
WDR5	PHF20L1	psi-mi:“MI:0914”(association)	0.350
PHF20L1	KANSL1L	psi-mi:“MI:0914”(association)	0.350
KANSL3	POTEF	psi-mi:“MI:0914”(association)	0.350
PHF20L1	PRKCA	psi-mi:“MI:0914”(association)	0.350
RBBP4	PHF20L1	psi-mi:“MI:0914”(association)	0.350
PHF20L1	gatA	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (105): ZNF471 (Two-hybrid), GATAD2B (Affinity Capture-MS), GATAD2A (Affinity Capture-MS), MBD2 (Affinity Capture-MS), MBD3 (Affinity Capture-MS), CHD4 (Affinity Capture-MS), CHD3 (Affinity Capture-MS), MTA2 (Affinity Capture-MS), MTA1 (Affinity Capture-MS), MTA3 (Affinity Capture-MS), RBBP7 (Affinity Capture-MS), KPNA4 (Affinity Capture-MS), LIN9 (Affinity Capture-MS), HDAC1 (Affinity Capture-MS), BCL11A (Affinity Capture-MS)

ESM2 similar proteins: A0AUZ9, A0JMF7, A1L2Y1, A3KMW7, A8MT70, A8MW92, A9JRX0, B0CM36, B0S6S9, B7ZS37, D3Z987, F1QB81, O95447, P40649, Q0IHW6, Q0P5X5, Q14B48, Q15468, Q3U285, Q3V089, Q49A88, Q4R815, Q4V9H5, Q5CZC0, Q5DTI6, Q5REF4, Q5T1N1, Q5ZJK5, Q66H35, Q6NRH7, Q6NRK3, Q6ZRS4, Q6ZU52, Q80VP2, Q80WQ8, Q8BLG0, Q8CB14, Q8CCJ9, Q8IUR6, Q8IX21

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, A6ZZW1, P36106, Q5XJV7, Q9C0A6, P42948, Q6IQX0, Q12830, Q9FEN9, Q9W0T1, Q9VW15, Q6L4L4, Q9FMS5, Q2LAE1, Q945S8, Q9M1X9, Q9VYD1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 21 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
HDACs deacetylate histones	5	46.2×	9e-06
HATs acetylate histones	5	30.5×	4e-05
Chromatin modifying enzymes	5	27.8×	4e-05

GO biological processes:

GO term	Partners	Fold	FDR
chromatin organization	5	31.0×	6e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4091 predictions. Top by Δscore:

Variant	Effect	Δscore
8:132777909:ATGGT:A	donor_loss	1.0000
8:132777910:TGG:T	donor_loss	1.0000
8:132777913:T:A	donor_loss	1.0000
8:132794582:G:GG	donor_gain	1.0000
8:132794815:AAGGT:A	donor_loss	1.0000
8:132794816:AGGT:A	donor_loss	1.0000
8:132794818:GTAT:G	donor_loss	1.0000
8:132794819:T:G	donor_loss	1.0000
8:132796086:C:G	donor_gain	1.0000
8:132796090:G:GG	donor_gain	1.0000
8:132799168:GTGAG:G	donor_gain	1.0000
8:132799170:GAGGT:G	donor_loss	1.0000
8:132799171:AGGT:A	donor_loss	1.0000
8:132799172:GGTA:G	donor_loss	1.0000
8:132799173:GT:G	donor_loss	1.0000
8:132799174:T:A	donor_loss	1.0000
8:132803814:T:TA	acceptor_gain	1.0000
8:132803815:G:A	acceptor_gain	1.0000
8:132804002:G:GT	donor_gain	1.0000
8:132811124:AGCAG:A	donor_loss	1.0000
8:132811125:GCAGG:G	donor_loss	1.0000
8:132811126:CAG:C	donor_loss	1.0000
8:132811127:AGGTA:A	donor_loss	1.0000
8:132811128:GGTAT:G	donor_loss	1.0000
8:132811129:G:A	donor_loss	1.0000
8:132814741:G:T	donor_gain	1.0000
8:132817025:A:T	donor_gain	1.0000
8:132817337:A:AG	acceptor_gain	1.0000
8:132817338:G:GG	acceptor_gain	1.0000
8:132817338:GT:G	acceptor_gain	1.0000

AlphaMissense

6749 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:132777865:T:C	F13L	1.000
8:132777866:T:C	F13S	1.000
8:132777867:T:A	F13L	1.000
8:132777867:T:G	F13L	1.000
8:132777910:T:A	W28R	1.000
8:132777910:T:C	W28R	1.000
8:132794410:G:C	W28C	1.000
8:132794410:G:T	W28C	1.000
8:132794424:T:A	I33N	1.000
8:132794424:T:G	I33S	1.000
8:132794460:T:A	V45D	1.000
8:132794462:C:G	H46D	1.000
8:132794465:T:C	F47L	1.000
8:132794466:T:C	F47S	1.000
8:132794466:T:G	F47C	1.000
8:132794467:T:A	F47L	1.000
8:132794467:T:G	F47L	1.000
8:132794474:T:A	W50R	1.000
8:132794474:T:C	W50R	1.000
8:132794476:G:C	W50C	1.000
8:132794476:G:T	W50C	1.000
8:132794495:T:A	W57R	1.000
8:132794495:T:C	W57R	1.000
8:132794497:G:C	W57C	1.000
8:132794497:G:T	W57C	1.000
8:132794504:T:A	W60R	1.000
8:132794504:T:C	W60R	1.000
8:132794520:T:C	L65S	1.000
8:132794755:T:A	V93D	1.000
8:132794758:T:C	L94P	1.000

dbSNP variants (sampled 300 via entrez): RS1000007249 (8:132795461 T>C), RS1000040964 (8:132841908 G>C,T), RS1000065723 (8:132807484 T>A), RS1000120277 (8:132788619 C>G), RS1000143051 (8:132834888 T>A), RS1000174104 (8:132800819 A>G), RS1000212118 (8:132815069 T>C), RS1000220367 (8:132843801 T>A,C,G), RS1000301433 (8:132821815 G>A), RS1000340133 (8:132829414 A>G), RS1000395785 (8:132807745 A>G), RS1000457418 (8:132794239 A>G), RS1000482263 (8:132847309 A>G), RS1000492408 (8:132788932 A>G), RS1000572462 (8:132844050 A>G)

Disease associations

OMIM: gene MIM:620050 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): Charcot-Marie-Tooth disease type 4 (MONDO:0018995)

Orphanet (1): Charcot-Marie-Tooth disease type 4 (Orphanet:64749)

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST009391_1485	Metabolite levels	9.000000e-06
GCST009391_1510	Metabolite levels	3.000000e-06
GCST009531_7	Body fat percentage	8.000000e-09
GCST010653_35	Thyroid stimulating hormone levels	8.000000e-22
GCST011773_33	Type 1 diabetes (age at diagnosis)	3.000000e-06
GCST90002396_442	Mean reticulocyte volume	4.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0010414	triacylglycerol 52:2 measurement
EFO:0010417	triacylglycerol 52:5 measurement
EFO:0007800	body fat percentage
EFO:0004918	age at diagnosis
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066242 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

50 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	6
bisphenol A	decreases methylation, increases expression, affects cotreatment, decreases expression	3
trichostatin A	affects cotreatment, decreases expression	3
entinostat	decreases expression, affects cotreatment	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	increases expression, decreases expression, affects cotreatment, increases abundance	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
methylmercuric chloride	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
aflatoxin B2	decreases methylation	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
bisphenol S	affects cotreatment, decreases expression	1
UNC1215	affects binding, decreases reaction	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Allergens	affects cotreatment, increases abundance, increases expression	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
Vehicle Emissions	affects cotreatment, increases abundance, increases expression	1
Coumestrol	affects cotreatment, decreases expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5712138	Binding	Binding affinity to tudor domain containing PHF20L1 (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 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_1661	ZR-75-30	Cancer cell line	Female

Clinical trials (associated diseases)

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