ZDHHC3

Summary

ZDHHC3 (zDHHC palmitoyltransferase 3, HGNC:18470) is a protein-coding gene on chromosome 3p21.31, encoding Palmitoyltransferase ZDHHC3 (Q9NYG2). Golgi-localized palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates.

Enables palmitoyltransferase activity. Involved in several processes, including protein localization to membrane; protein localization to photoreceptor outer segment; and regulation of signal transduction. Located in membrane. Is active in Golgi apparatus.

Source: NCBI Gene 51304 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 34 total
• Druggable target: yes
• MANE Select transcript: NM_001135179

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18470
Approved symbol	ZDHHC3
Name	zDHHC palmitoyltransferase 3
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	ZNF373, GODZ, DHHC3
Ensembl gene	ENSG00000163812
Ensembl biotype	protein_coding
OMIM	617150
Entrez	51304

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 24 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000296127, ENST00000339420, ENST00000342790, ENST00000419642, ENST00000424952, ENST00000433512, ENST00000443879, ENST00000455235, ENST00000466084, ENST00000478669, ENST00000479314, ENST00000705994, ENST00000906159, ENST00000906160, ENST00000906161, ENST00000906162, ENST00000906163, ENST00000906164, ENST00000906165, ENST00000906166, ENST00000906167, ENST00000906168, ENST00000906169, ENST00000906170, ENST00000906171, ENST00000906172, ENST00000931780, ENST00000960554, ENST00000960555

RefSeq mRNA: 9 — MANE Select: NM_001135179 NM_001135179, NM_001330761, NM_001349376, NM_001349377, NM_001349378, NM_001349379, NM_001349380, NM_001349381, NM_016598

CCDS: CCDS2724, CCDS46810, CCDS46811, CCDS87071, CCDS93256

Canonical transcript exons

ENST00000424952 — 7 exons

Exon	Start	End
ENSE00001078524	44933118	44933199
ENSE00001846897	44975933	44976174
ENSE00001920311	44915261	44926847
ENSE00003540377	44959131	44959460
ENSE00003563190	44945168	44945292
ENSE00003622187	44933888	44933984
ENSE00003789882	44929306	44929436

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 97.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.5205 / max 356.9954, expressed in 1821 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41873	28.1283	1821
41871	0.1858	61
41870	0.1293	44
41866	0.0274	3
41872	0.0191	4
41869	0.0158	2
41865	0.0148	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	97.54	gold quality
right testis	UBERON:0004534	97.46	gold quality
rectum	UBERON:0001052	96.27	gold quality
stromal cell of endometrium	CL:0002255	96.10	gold quality
skin of leg	UBERON:0001511	95.23	gold quality
testis	UBERON:0000473	95.18	gold quality
left adrenal gland	UBERON:0001234	95.06	gold quality
sperm	CL:0000019	95.03	gold quality
right adrenal gland	UBERON:0001233	95.03	gold quality
skin of abdomen	UBERON:0001416	95.03	gold quality
left adrenal gland cortex	UBERON:0035825	94.87	gold quality
right adrenal gland cortex	UBERON:0035827	94.71	gold quality
mucosa of transverse colon	UBERON:0004991	94.69	gold quality
esophagus mucosa	UBERON:0002469	94.34	gold quality
adrenal gland	UBERON:0002369	94.06	gold quality
zone of skin	UBERON:0000014	93.94	gold quality
adrenal cortex	UBERON:0001235	93.81	gold quality
male germ cell	CL:0000015	93.80	gold quality
gall bladder	UBERON:0002110	93.58	gold quality
transverse colon	UBERON:0001157	93.46	gold quality
upper lobe of left lung	UBERON:0008952	93.24	gold quality
esophagus	UBERON:0001043	93.10	gold quality
upper lobe of lung	UBERON:0008948	92.89	gold quality
hindlimb stylopod muscle	UBERON:0004252	92.86	gold quality
ectocervix	UBERON:0012249	92.77	gold quality
omental fat pad	UBERON:0010414	92.56	gold quality
peritoneum	UBERON:0002358	92.51	gold quality
right lung	UBERON:0002167	92.40	gold quality
adipose tissue of abdominal region	UBERON:0007808	92.34	gold quality
popliteal artery	UBERON:0002250	92.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.61

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

421 targeting ZDHHC3, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3662	99.99	73.82	5684

Literature-anchored findings (GeneRIF, showing 9)

• Data conclude that GODZ encodes a Ca(2+) transport protein in addition to its ability to palmitoylate protein substrates. (PMID:19955568)
• GODZ regulates plasma membrane targeting of DR4 and thus TRAIL/DR4-mediated apoptosis in cancer cells. (PMID:22240897)
• Palmitoylation by DHHC3 is critical for the function, expression, and stability of integrin alpha6beta4. (PMID:22314500)
• In silico screening for palmitoyl substrates reveals a role for DHHC1/3/10 (zDHHC1/3/11)-mediated neurochondrin palmitoylation in its targeting to Rab5-positive endosomes. (PMID:23687301)
• HSV-1 UL20 binds to GODZ (also known as DHHC3), a Golgi apparatus-specific Asp-His-His-Cys (DHHC) zinc finger protein. a GODZ dominant-negative mutant and an inhibitor of palmitoylation reduced HSV-1 titers and altered the localization of UL20 and glycoprotein K. UL20 is palmitoylated by GODZ, and this UL20 palmitoylation is required for HSV-1 infectivity. (PMID:28724772)
• DHHC3-mediated protein palmitoylation supports breast tumor growth by modulating cellular oxidative stress and senescence. (PMID:29055014)
• Antioxidant functions of DHHC3 suppress anti-cancer drug activities. (PMID:32986127)
• IFI27 Integrates Succinate and Fatty Acid Oxidation to Promote Adipocyte Thermogenic Adaption. (PMID:37544897)
• zDHHC3-mediated S-palmitoylation of SLC9A2 regulates apoptosis in kidney clear cell carcinoma. (PMID:38619631)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zdhhc3a	ENSDARG00000010981
mus_musculus	Zdhhc3	ENSMUSG00000025786
rattus_norvegicus	Zdhhc3	ENSRNOG00000004344
drosophila_melanogaster	CG8314	FBGN0034057
caenorhabditis_elegans	dhhc-3	WBGENE00018009

Paralogs (17): ZDHHC6 (ENSG00000023041), ZDHHC15 (ENSG00000102383), ZDHHC2 (ENSG00000104219), ZDHHC4 (ENSG00000136247), ZDHHC7 (ENSG00000153786), ZDHHC1 (ENSG00000159714), ZDHHC12 (ENSG00000160446), ZDHHC19 (ENSG00000163958), ZDHHC14 (ENSG00000175048), ZDHHC21 (ENSG00000175893), ZDHHC22 (ENSG00000177108), ZDHHC20 (ENSG00000180776), ZDHHC23 (ENSG00000184307), ZDHHC9 (ENSG00000188706), ZDHHC11 (ENSG00000188818), ZDHHC18 (ENSG00000204160), ZDHHC11B (ENSG00000206077)

Protein

Protein identifiers

Palmitoyltransferase ZDHHC3 — Q9NYG2 (reviewed: Q9NYG2)

Alternative names: Acyltransferase ZDHHC3, Protein DHHC1, Zinc finger DHHC domain-containing protein 3

All UniProt accessions (7): A0A994J7J2, C9JNU5, Q9NYG2, F8W6M3, H0Y6A5, H7C1U6, H7C365

UniProt curated annotations — full annotation on UniProt →

Function. Golgi-localized palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates. Has no stringent fatty acid selectivity and in addition to palmitate can also transfer onto target proteins myristate from tetradecanoyl-CoA and stearate from octadecanoyl-CoA. Plays an important role in G protein-coupled receptor signaling pathways involving GNAQ and potentially other heterotrimeric G proteins by regulating their dynamic association with the plasma membrane. Palmitoylates ITGA6 and ITGB4, thereby regulating the alpha-6/beta-4 integrin localization, expression and function in cell adhesion to laminin. Plays a role in the TRAIL-activated apoptotic signaling pathway most probably through the palmitoylation and localization to the plasma membrane of TNFRSF10A. In the brain, by palmitoylating the gamma subunit GABRG2 of GABA(A) receptors and regulating their postsynaptic accumulation, plays a role in synaptic GABAergic inhibitory function and GABAergic innervation. Palmitoylates the neuronal protein GAP43 which is also involved in the formation of GABAergic synapses. Palmitoylates NCDN thereby regulating its association with endosome membranes. Probably palmitoylates PRCD and is involved in its proper localization within the photoreceptor. Could mediate the palmitoylation of NCAM1 and regulate neurite outgrowth. Could palmitoylate DNAJC5 and regulate its localization to Golgi membranes. Also constitutively palmitoylates DLG4. May also palmitoylate SNAP25. Could palmitoylate the glutamate receptors GRIA1 and GRIA2 but this has not been confirmed in vivo. Could also palmitoylate the D(2) dopamine receptor DRD2. May also palmitoylate LAMTOR1, promoting its localization to lysosomal membranes. Palmitoylates the Toll-like receptor 9/TLR9 in the Golgi and thereby regulates TLR9 trafficking to endosomes. May palmitoylate CALHM1 and CALHM3 subunits of gustatory voltage-gated ion channels and modulate channel gating and kinetics. May also function as a calcium transporter.

Subunit / interactions. Monomer. Homooligomers. The monomeric form has a higher catalytic activity. Forms heterooligomers with ZDHHC7. Interacts with TNFRSF10A.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Widely expressed with significant expression in heart, lung, liver, skeletal muscle, kidney, testis, thymus, small intestine and leukocyte.

Post-translational modifications. Autopalmitoylated. Phosphorylation by FGFR1 and SRC probably regulates the palmitoyltransferase activity.

Domain organisation. The DHHC domain is required for palmitoyltransferase activity.

Similarity. Belongs to the DHHC palmitoyltransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NYG2-1	1	yes
Q9NYG2-2	2

RefSeq proteins (9): NP_001128651, NP_001317690, NP_001336305, NP_001336306, NP_001336307, NP_001336308, NP_001336309, NP_001336310, NP_057682 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001594	Palmitoyltrfase_DHHC	Domain
IPR039859	PFA4/ZDH16/20/ERF2-like	Family

Pfam: PF01529

Enzyme classification (BRENDA):

• EC 2.3.1.225 — protein S-acyltransferase (BRENDA: 9 organisms, 108 substrates, 15 inhibitors, 6 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
PALMITOYL-COA	0.0052–0.0059	2
[N-MYRISTOYLATED GLY-CYS-GLY TRIPEPTIDE]-L-CYSTE	0.0008–0.0013	2

Catalyzed reactions (Rhea), 3 shown:

• L-cysteinyl-[protein] + hexadecanoyl-CoA = S-hexadecanoyl-L-cysteinyl-[protein] + CoA (RHEA:36683)
• L-cysteinyl-[protein] + tetradecanoyl-CoA = S-tetradecanoyl-L-cysteinyl-[protein] + CoA (RHEA:59736)
• L-cysteinyl-[protein] + octadecanoyl-CoA = S-octadecanoyl-L-cysteinyl-[protein] + CoA (RHEA:59740)

UniProt features (18 total): topological domain 5, transmembrane region 4, mutagenesis site 3, chain 1, domain 1, active site 1, modified residue 1, lipid moiety-binding region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NYG2-F1	85.25	0.63

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 157 (s-palmitoyl cysteine intermediate)

Post-translational modifications (2): 18, 146

Mutagenesis-validated functional residues (3):

Position	Phenotype
155	probable loss of protein-cysteine s-palmitoyltransferase activity. loss of function in the trail-activated apoptotic sig
157	probable loss of protein-cysteine s-palmitoyltransferase activity. loss of function in the trail-activated apoptotic sig
299	impaired localization leading to localization to the endoplasmic reticulum.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9694548	Maturation of spike protein

MSigDB gene sets: 244 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_LIPOPROTEIN_METABOLIC_PROCESS, GOBP_TOLL_LIKE_RECEPTOR_9_SIGNALING_PATHWAY, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_PROTEIN_TARGETING, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_PEPTIDYL_CYSTEINE_MODIFICATION, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_CELL_CELL_SIGNALING, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, COUP_01, GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS

GO Biological Process (17): protein targeting to membrane (GO:0006612), regulation of G protein-coupled receptor signaling pathway (GO:0008277), peptidyl-L-cysteine S-palmitoylation (GO:0018230), protein palmitoylation (GO:0018345), positive regulation of synaptic transmission, GABAergic (GO:0032230), positive regulation of toll-like receptor 9 signaling pathway (GO:0034165), TRAIL-activated apoptotic signaling pathway (GO:0036462), lipoprotein localization to membrane (GO:0044873), protein localization to membrane (GO:0072657), protein localization to plasma membrane (GO:0072659), positive regulation of receptor localization to synapse (GO:1902685), protein localization to photoreceptor outer segment (GO:1903546), protein targeting (GO:0006605), cellular response to nutrient levels (GO:0031669), toll-like receptor 9 signaling pathway (GO:0034162), positive regulation of protein localization to lysosome (GO:0150032), positive regulation of TORC1 signaling (GO:1904263)

GO Molecular Function (7): palmitoyltransferase activity (GO:0016409), protein-cysteine S-myristoyltransferase activity (GO:0019705), protein-cysteine S-palmitoyltransferase activity (GO:0019706), protein homodimerization activity (GO:0042803), protein-cysteine S-stearoyltransferase activity (GO:0140439), transferase activity (GO:0016740), acyltransferase activity (GO:0016746)

GO Cellular Component (4): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Translation of Structural Proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein-cysteine S-acyltransferase activity	3
localization within membrane	2
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
protein targeting	1
establishment of protein localization to membrane	1
G protein-coupled receptor signaling pathway	1
regulation of signal transduction	1
peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine	1
protein palmitoylation	1
protein lipidation	1
protein acylation	1
regulation of synaptic transmission, GABAergic	1
positive regulation of synaptic transmission	1
synaptic transmission, GABAergic	1
toll-like receptor 9 signaling pathway	1
regulation of toll-like receptor 9 signaling pathway	1
positive regulation of pattern recognition receptor signaling pathway	1
positive regulation of intracellular signal transduction	1
extrinsic apoptotic signaling pathway via death domain receptors	1
lipoprotein localization	1
intracellular protein localization	1
protein localization to membrane	1
protein localization to cell periphery	1
positive regulation of biological process	1
receptor localization to synapse	1
regulation of receptor localization to synapse	1
protein localization to non-motile cilium	1
establishment of protein localization	1
response to nutrient levels	1
cellular response to stimulus	1
endolysosomal toll-like receptor signaling pathway	1
protein localization to lysosome	1
regulation of protein localization to lysosome	1
positive regulation of protein localization	1
positive regulation of TOR signaling	1
TORC1 signaling	1
regulation of TORC1 signaling	1
acyltransferase activity, transferring groups other than amino-acyl groups	1

Protein interactions and networks

STRING

896 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZDHHC3	ZDHHC11	Q9H8X9	645
ZDHHC3	ZDHHC13	Q8IUH4	614
ZDHHC3	ZDHHC17	Q8IUH5	590
ZDHHC3	GABARAP	O95166	587
ZDHHC3	ZDHHC16	Q969W1	542
ZDHHC3	GOLGA7	Q7Z5G4	524
ZDHHC3	ZDHHC14	Q8IZN3	506
ZDHHC3	PPT1	P50897	505
ZDHHC3	LYPLA2	O95372	487
ZDHHC3	DLG4	P78352	479
ZDHHC3	ZDHHC8	Q9ULC8	465
ZDHHC3	LYPLA1	O75608	461
ZDHHC3	ABHD17A	Q96GS6	448
ZDHHC3	GPHN	Q9NQX3	437
ZDHHC3	EPB41L1	Q9H4G0	434

IntAct

18 interactions, top by confidence:

A	B	Type	Score
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
S	ZDHHC3	psi-mi:“MI:0216”(palmitoylation reaction)	0.440
ZDHHC3	GPR35	psi-mi:“MI:0915”(physical association)	0.370
SMAD1	ZDHHC3	psi-mi:“MI:0915”(physical association)	0.370
EWSR1	ZDHHC3	psi-mi:“MI:0915”(physical association)	0.370
	TMEM223	psi-mi:“MI:0914”(association)	0.350
COPB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
GORASP2	PGRMC1	psi-mi:“MI:0914”(association)	0.350
TMED10	PGRMC1	psi-mi:“MI:0914”(association)	0.350
HCST	TMEM120B	psi-mi:“MI:0914”(association)	0.350
SCAP	UPK3BL1	psi-mi:“MI:0914”(association)	0.350
SLC34A2	SYNGR2	psi-mi:“MI:0914”(association)	0.350
C1orf210	IPO7	psi-mi:“MI:0914”(association)	0.350
HLA-C	TMEM131L	psi-mi:“MI:0914”(association)	0.350
ZDHHC3	pntA	psi-mi:“MI:0915”(physical association)	0.000
UBQLN4	ZDHHC3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (34): ZDHHC3 (Two-hybrid), ZDHHC3 (Affinity Capture-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Proximity Label-MS), ZDHHC3 (Two-hybrid), ZDHHC3 (Affinity Capture-MS), ZDHHC3 (Affinity Capture-MS), ZDHHC3 (Affinity Capture-MS), ZDHHC3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0R4IQZ2, A5WVX9, B1H1H3, E7F587, E9PTT0, F1QAM1, F1QGD2, P0CS66, P0CS67, P42836, Q09701, Q12013, Q2HJ95, Q2TGJ4, Q2TGK3, Q3EC11, Q4I8B6, Q4R690, Q4X251, Q52T38, Q58DT3, Q5B0V6, Q5BLG4, Q5FWL7, Q5NVB9, Q5REH2, Q6C4W5, Q6C520, Q6DHI1, Q750R7, Q755Y0, Q75AW7, Q7S3M5, Q7Z8U2, Q80TN5, Q875M2, Q8BGJ0, Q8IUH4, Q8IUH5, Q8R173

Diamond homologs: A0A0R4IDP3, A2CEX1, A2VEY9, A5WVX9, B3DN87, C8VCL4, E1BLT8, E7F021, E7F587, E7FBS9, E7FH11, E9PTT0, E9QCD3, F1Q7H8, F1QAM1, F1QHM7, F1QX91, F1QXD3, F1R013, F1RE57, J9VJ99, O60069, O74384, O80685, P42836, P59267, P59268, Q04629, Q0VC89, Q10L01, Q2TGJ1, Q2TGJ4, Q2TGK3, Q2THW7, Q2THW8, Q2THW9, Q2THX0, Q2THX1, Q4R690, Q4WZL8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1724 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44929301:CTTA:C	donor_loss	1.0000
3:44929302:TTACC:T	donor_loss	1.0000
3:44929303:TACCG:T	donor_loss	1.0000
3:44929305:C:A	donor_loss	1.0000
3:44929305:CCGT:C	donor_gain	1.0000
3:44929435:CT:C	acceptor_gain	1.0000
3:44933112:A:AC	donor_gain	1.0000
3:44933113:C:CC	donor_gain	1.0000
3:44933113:CTCA:C	donor_gain	1.0000
3:44933114:TCAC:T	donor_loss	1.0000
3:44933115:CA:C	donor_loss	1.0000
3:44933116:A:AC	donor_gain	1.0000
3:44933117:C:CC	donor_gain	1.0000
3:44933117:CTTGT:C	donor_gain	1.0000
3:44945162:GTGTA:G	donor_loss	1.0000
3:44945163:TGTA:T	donor_loss	1.0000
3:44945164:GTAC:G	donor_loss	1.0000
3:44945165:TACCT:T	donor_loss	1.0000
3:44945166:A:C	donor_loss	1.0000
3:44945167:C:G	donor_loss	1.0000
3:44945289:CCCC:C	acceptor_gain	1.0000
3:44945290:CCC:C	acceptor_gain	1.0000
3:44945290:CCCC:C	acceptor_gain	1.0000
3:44945291:CC:C	acceptor_gain	1.0000
3:44945291:CCC:C	acceptor_gain	1.0000
3:44945292:CC:C	acceptor_gain	1.0000
3:44945292:CCT:C	acceptor_loss	1.0000
3:44959125:A:AC	donor_gain	1.0000
3:44959126:C:CC	donor_gain	1.0000
3:44959126:CTCA:C	donor_gain	1.0000

AlphaMissense

1986 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44926751:A:G	W280R	1.000
3:44926751:A:T	W280R	1.000
3:44929357:G:C	F230L	1.000
3:44929357:G:T	F230L	1.000
3:44929359:A:G	F230L	1.000
3:44929366:G:C	F227L	1.000
3:44929366:G:T	F227L	1.000
3:44929368:A:G	F227L	1.000
3:44933891:A:C	F175L	1.000
3:44933891:A:T	F175L	1.000
3:44933893:A:G	F175L	1.000
3:44933893:A:T	F175I	1.000
3:44933895:A:G	L174P	1.000
3:44933900:G:C	F172L	1.000
3:44933900:G:T	F172L	1.000
3:44933901:A:C	F172C	1.000
3:44933901:A:G	F172S	1.000
3:44933902:A:G	F172L	1.000
3:44933912:G:C	N168K	1.000
3:44933912:G:T	N168K	1.000
3:44933922:C:A	G165V	1.000
3:44933922:C:T	G165D	1.000
3:44933923:C:G	G165R	1.000
3:44933925:A:T	V164E	1.000
3:44933927:A:C	C163W	1.000
3:44933928:C:A	C163F	1.000
3:44933928:C:G	C163S	1.000
3:44933928:C:T	C163Y	1.000
3:44933929:A:G	C163R	1.000
3:44933929:A:T	C163S	1.000

dbSNP variants (sampled 300 via entrez): RS1000006388 (3:44920915 T>C), RS1000011678 (3:44942487 G>C), RS1000068135 (3:44951913 C>G,T), RS1000147175 (3:44938353 A>C,G), RS1000178920 (3:44922626 G>A,C), RS1000226129 (3:44974522 C>T), RS1000352085 (3:44975945 G>A,C), RS1000370567 (3:44931833 G>A), RS1000418569 (3:44944768 A>T), RS1000461922 (3:44936139 T>A,C), RS1000482612 (3:44945404 A>C), RS1000487909 (3:44976114 C>G), RS1000492912 (3:44926004 T>C), RS1000542550 (3:44923680 G>A), RS1000543869 (3:44925773 T>C)

Disease associations

OMIM: gene MIM:617150 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002481_7	Acne (severe)	3.000000e-06
GCST007130_1	Cerebrospinal fluid t-tau:AB1-42 ratio	5.000000e-09
GCST007666_4	Depressive symptom improvement	7.000000e-07
GCST008103_52	Bipolar disorder	3.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007708	t-tau:beta-amyloid 1-42 ratio measurement
EFO:0007006	depressive symptom measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067466 (SINGLE PROTEIN)

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

PharmGKB clinical annotations

1 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs3749187	Efficacy	3	aspirin;clopidogrel	Acute coronary syndrome;Major Adverse Cardiac Events (MACE)

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs3749187	ZDHHC3	3	3.50	1	aspirin;clopidogrel

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — 2.3.1.- Acyltransferases

Most potent curated ligand interactions (1 total), top 1:

Ligand	Action	Affinity	Parameter
benzosceptrin C	Binding	6.41	pKd

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Arsenic	decreases expression, increases abundance, affects methylation, affects cotreatment	2
bisphenol F	affects cotreatment, increases expression	1
TAK-243	affects sumoylation	1
triphenyl phosphate	affects expression	1
sulforaphane	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	increases expression	1
Temozolomide	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Carbamazepine	affects expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylstilbestrol	increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	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
CHEMBL5524587	Binding	Inhibition of ZDHHC3 (unknown origin)	Modulators for palmitoylation of proteins and small molecules. — Eur J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TY94	HAP1 ZDHHC3 (-) 1	Cancer cell line	Male
CVCL_TY95	HAP1 ZDHHC3 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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