ZNF385D

Summary

ZNF385D (zinc finger protein 385D, HGNC:26191) is a protein-coding gene on chromosome 3p24.3, encoding Zinc finger protein 385D (Q9H6B1).

Enables sequence-specific double-stranded DNA binding activity. Predicted to be active in nucleus.

Source: NCBI Gene 79750 — RefSeq curated summary.

At a glance

• GWAS associations: 26
• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_024697

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26191
Approved symbol	ZNF385D
Name	zinc finger protein 385D
Location	3p24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22419
Ensembl gene	ENSG00000151789
Ensembl biotype	protein_coding
OMIM	621200
Entrez	79750

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 9 nonsense_mediated_decay, 7 protein_coding, 6 protein_coding_CDS_not_defined

ENST00000281523, ENST00000446749, ENST00000466511, ENST00000467140, ENST00000469927, ENST00000474607, ENST00000478967, ENST00000494108, ENST00000494118, ENST00000495739, ENST00000497570, ENST00000706131, ENST00000706132, ENST00000706133, ENST00000706134, ENST00000706135, ENST00000706136, ENST00000706137, ENST00000706138, ENST00000706139, ENST00000871533, ENST00000963857

RefSeq mRNA: 1 — MANE Select: NM_024697 NM_024697

CCDS: CCDS2636

Canonical transcript exons

ENST00000281523 — 8 exons

Exon	Start	End
ENSE00001001781	21436970	21437203
ENSE00001203721	21750895	21751210
ENSE00001909889	21412218	21421447
ENSE00003493731	21510861	21511023
ENSE00003543799	21664886	21665028
ENSE00003544734	21564574	21564684
ENSE00003617762	21423963	21424064
ENSE00003644743	21425492	21425670

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 95.79.

FANTOM5 (CAGE): breadth broad, TPM avg 4.8370 / max 451.5748, expressed in 796 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41427	1.2806	434
41425	1.0536	510
41426	0.5754	328
41454	0.5037	83
41429	0.4728	249
41452	0.3622	84
41449	0.2105	32
41428	0.1549	83
41451	0.0548	17
41430	0.0542	24

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
descending thoracic aorta	UBERON:0002345	95.79	gold quality
ascending aorta	UBERON:0001496	95.01	gold quality
thoracic aorta	UBERON:0001515	95.00	gold quality
tendon of biceps brachii	UBERON:0008188	94.55	gold quality
cartilage tissue	UBERON:0002418	91.39	gold quality
endothelial cell	CL:0000115	91.10	gold quality
left testis	UBERON:0004533	89.76	gold quality
right testis	UBERON:0004534	89.39	gold quality
aorta	UBERON:0000947	88.80	gold quality
left coronary artery	UBERON:0001626	88.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.40	gold quality
tendon	UBERON:0000043	87.74	gold quality
calcaneal tendon	UBERON:0003701	87.36	gold quality
testis	UBERON:0000473	87.17	gold quality
coronary artery	UBERON:0001621	87.16	gold quality
Brodmann (1909) area 23	UBERON:0013554	86.59	gold quality
right coronary artery	UBERON:0001625	86.31	gold quality
cerebellar cortex	UBERON:0002129	85.17	gold quality
cerebellar hemisphere	UBERON:0002245	85.02	gold quality
middle temporal gyrus	UBERON:0002771	84.99	gold quality
omental fat pad	UBERON:0010414	84.87	gold quality
peritoneum	UBERON:0002358	84.80	gold quality
lower esophagus muscularis layer	UBERON:0035833	84.74	gold quality
lower esophagus	UBERON:0013473	84.68	gold quality
cortical plate	UBERON:0005343	84.56	gold quality
cerebellum	UBERON:0002037	84.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.39	gold quality
popliteal artery	UBERON:0002250	84.31	gold quality
tibial artery	UBERON:0007610	84.26	gold quality
blood vessel layer	UBERON:0004797	84.19	gold quality

Single-cell (SCXA)

Detected in 16 experiment(s), a significant marker in 14.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	15656.47
E-HCAD-35	yes	3710.81
E-HCAD-25	yes	3461.90
E-HCAD-30	yes	2977.31
E-MTAB-9154	yes	2043.31
E-MTAB-8142	yes	153.16
E-ENAD-27	yes	101.10
E-CURD-119	yes	47.32
E-GEOD-135922	yes	33.54
E-ANND-3	yes	26.85
E-GEOD-81608	yes	17.44
E-GEOD-81547	yes	11.24
E-GEOD-137537	yes	8.27
E-MTAB-8410	yes	3.94
E-HCAD-5	no	2180.34

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXO3

miRNA regulators (miRDB)

39 targeting ZNF385D, 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-5692A	100.00	74.40	6850
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-7844-5P	99.55	68.56	1428
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-6507-3P	99.35	67.32	1059
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-5584-3P	99.23	68.79	1351
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-5100	99.11	67.52	1098
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-3916	98.99	68.04	2155

Literature-anchored findings (GeneRIF, showing 1)

• ZNF385D is a candidate gene for reading disability and language impairment. (PMID:24024963)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf385d	ENSDARG00000086162
drosophila_melanogaster	CG1231	FBGN0035134
drosophila_melanogaster	dbf	FBGN0287630

Paralogs (9): ZNF346 (ENSG00000113761), ZNF385B (ENSG00000144331), ZMAT2 (ENSG00000146007), ZNF385A (ENSG00000161642), ZMAT4 (ENSG00000165061), ZMAT1 (ENSG00000166432), KRCC1 (ENSG00000172086), ZMAT3 (ENSG00000172667), ZNF385C (ENSG00000187595)

Protein

Protein identifiers

Zinc finger protein 385D — Q9H6B1 (reviewed: Q9H6B1)

Alternative names: Zinc finger protein 659

All UniProt accessions (13): Q9H6B1, A0A2R8Y4E5, A0A2R8YG37, A0A3B3IUA5, A0A994J524, A0A994J528, A0A994J5B7, A0A994J5C1, A0A994J5P6, A0A994J5Q0, A0A994J7K4, A0A994J7Y4, F8WEJ0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (1): NP_078973* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR051845	Znf385	Family

Pfam: PF12874

UniProt features (9 total): zinc finger region 3, region of interest 2, sequence variant 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6B1-F1	62.68	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, BOQUEST_STEM_CELL_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chr3p24, CBX7_TARGET_GENES, MIR6809_3P, MIR9983_3P, MIR4753_3P, MIR137_3P, MIR129_5P, MIR32_5P, MIR92A_3P, MIR8068, MIR92B_3P, MIR4531

GO Biological Process (0):

GO Molecular Function (4): zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), nucleic acid binding (GO:0003676), metal ion binding (GO:0046872)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

566 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF385D	CCDC136	Q96JN2	577
ZNF385D	NDST4	Q9H3R1	523
ZNF385D	DNAAF4	Q8WXU2	513
ZNF385D	KIAA0319	Q5VV43	506
ZNF385D	CMIP	Q8IY22	483
ZNF385D	ATP2C2	O75185	482
ZNF385D	DCDC2	Q9UHG0	462
ZNF385D	PGBD2	Q6P3X8	447
ZNF385D	RBFOX2	O43251	433
ZNF385D	NFXL1	Q6ZNB6	370
ZNF385D	ZNF677	Q86XU0	370
ZNF385D	CNTNAP2	Q9UHC6	369
ZNF385D	CCPG1	Q9ULG6	368
ZNF385D	COL4A2	P08572	364
ZNF385D	TRPC4AP	Q8TEL6	353

IntAct

2 interactions, top by confidence:

A	B	Type	Score
ZNF385D	RPL15	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): ZNF385D (Proximity Label-MS), ZNF385D (Affinity Capture-RNA)

ESM2 similar proteins: A2A5E6, A5PK23, A6NKF2, A6PWV5, B0K011, E9Q6W4, O02786, O95402, P09086, P13297, P55198, Q00196, Q08DS3, Q0VDQ9, Q29013, Q2NKI2, Q2VL80, Q2VL82, Q2VL83, Q2VL85, Q2VL86, Q569K4, Q5XI28, Q62255, Q66K41, Q6AXX3, Q6PBT9, Q86V15, Q8BXJ8, Q8IVH2, Q8K4J6, Q8TAX0, Q8VD12, Q8VDL9, Q8WUU4, Q92766, Q969V6, Q96PM9, Q9BXA9, Q9BZE0

Diamond homologs: A2A5E6, Q569K4, Q66K41, Q6AXX3, Q6PBT9, Q8AVN9, Q8BXJ8, Q8VD12, Q96PM9, Q9H6B1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	73
Likely benign	0
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

3124 predictions. Top by Δscore:

Variant	Effect	Δscore
3:21436969:CCA:C	donor_gain	1.0000
3:21437053:T:TA	donor_gain	1.0000
3:21437200:CCGT:C	acceptor_gain	1.0000
3:21437201:CGT:C	acceptor_gain	1.0000
3:21437201:CGTC:C	acceptor_gain	1.0000
3:21437202:GT:G	acceptor_gain	1.0000
3:21437203:TC:T	acceptor_loss	1.0000
3:21437204:C:CC	acceptor_gain	1.0000
3:21437211:C:CT	acceptor_gain	1.0000
3:21437212:A:T	acceptor_gain	1.0000
3:21437215:A:AC	acceptor_gain	1.0000
3:21437215:A:C	acceptor_gain	1.0000
3:21437219:C:CT	acceptor_gain	1.0000
3:21437221:C:CT	acceptor_gain	1.0000
3:21437222:A:T	acceptor_gain	1.0000
3:21510858:AAC:A	donor_gain	1.0000
3:21510859:A:C	donor_gain	1.0000
3:21511019:TGGCT:T	acceptor_gain	1.0000
3:21511020:GGCT:G	acceptor_gain	1.0000
3:21511022:CT:C	acceptor_gain	1.0000
3:21511023:TC:T	acceptor_loss	1.0000
3:21511024:C:CC	acceptor_gain	1.0000
3:21511025:T:C	acceptor_loss	1.0000
3:21564572:A:AC	donor_gain	1.0000
3:21564573:C:CC	donor_gain	1.0000
3:21564573:CAT:C	donor_gain	1.0000
3:21564591:A:C	donor_gain	1.0000
3:21564681:CCAT:C	acceptor_gain	1.0000
3:21564682:CAT:C	acceptor_gain	1.0000
3:21564682:CATC:C	acceptor_gain	1.0000

AlphaMissense

2567 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:21424040:C:G	D293H	1.000
3:21424041:T:A	K292N	1.000
3:21424041:T:G	K292N	1.000
3:21424043:T:C	K292E	1.000
3:21424044:G:C	H291Q	1.000
3:21424044:G:T	H291Q	1.000
3:21424045:T:C	H291R	1.000
3:21424046:G:C	H291D	1.000
3:21424046:G:T	H291N	1.000
3:21424047:C:A	R290S	1.000
3:21424047:C:G	R290S	1.000
3:21424048:C:A	R290M	1.000
3:21424048:C:G	R290T	1.000
3:21424050:T:A	R289S	1.000
3:21424050:T:G	R289S	1.000
3:21424051:C:A	R289I	1.000
3:21424051:C:G	R289T	1.000
3:21424052:T:C	R289G	1.000
3:21424053:A:C	S288R	1.000
3:21424053:A:T	S288R	1.000
3:21424054:C:A	S288I	1.000
3:21424054:C:T	S288N	1.000
3:21424055:T:G	S288R	1.000
3:21424060:A:T	I286N	1.000
3:21424062:G:C	H285Q	1.000
3:21424062:G:T	H285Q	1.000
3:21424063:T:A	H285L	1.000
3:21424063:T:C	H285R	1.000
3:21424063:T:G	H285P	1.000
3:21424064:G:A	H285Y	1.000

dbSNP variants (sampled 300 via entrez): RS1000002109 (3:22075224 C>T), RS1000004343 (3:21674882 G>A), RS1000006494 (3:22294527 G>C,T), RS1000007709 (3:21695385 T>C), RS1000009904 (3:21708674 T>A), RS1000010191 (3:22216044 G>A,C), RS1000012489 (3:22126378 A>C), RS1000013813 (3:21770771 T>C), RS1000015791 (3:22308048 G>A), RS1000016828 (3:22370612 G>A,C), RS1000018977 (3:21734490 A>G), RS1000021404 (3:22029641 C>T), RS1000022751 (3:21934584 A>G), RS1000028548 (3:21738405 C>T), RS1000030123 (3:22325254 A>C)

Disease associations

OMIM: gene MIM:621200 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

26 associations (top):

Study	Trait	p-value
GCST000691_3	Partial epilepsies	5.000000e-06
GCST001838_3	Palmitic acid (16:0) levels	5.000000e-06
GCST002136_13	Periodontitis (PAL4Q3)	6.000000e-06
GCST002794_11	Airway wall thickness	8.000000e-06
GCST003263_19	Post bronchodilator FEV1 in COPD	2.000000e-06
GCST003264_118	Post bronchodilator FEV1/FVC ratio	2.000000e-06
GCST003518_27	Daytime sleep phenotypes	2.000000e-07
GCST003518_41	Daytime sleep phenotypes	5.000000e-08
GCST003941_1	Acute graft versus host disease in bone marrow transplantation (recipient effect)	7.000000e-10
GCST004162_34	Carotid plaque burden	4.000000e-06
GCST004583_1	Waist-to-hip circumference ratio (recreational physical activity interaction)	2.000000e-06
GCST006865_7	Bipolar disorder	5.000000e-06
GCST007467_6	Word spelling	2.000000e-06
GCST008923_1	Ceramide levels	4.000000e-09
GCST008923_5	Ceramide levels	7.000000e-09
GCST008923_7	Ceramide levels	5.000000e-09
GCST009175_2	Caudal anterior-cingulate cortex volume	1.000000e-06
GCST009391_1288	Metabolite levels	7.000000e-06
GCST009462_44	Optic disc size	2.000000e-08
GCST011739_1	Cutaneous leishmaniasis	2.000000e-06
GCST011946_14	White matter hyperintensity volume	4.000000e-06
GCST011947_16	White matter hyperintensity volume	1.000000e-06
GCST011949_30	White matter hyperintensity volume (adjusted for hypertension)	3.000000e-06
GCST011950_6	White matter hyperintensity volume (adjusted for hypertension)	1.000000e-06
GCST011952_24	White matter hyperintensity volume x hypertension interaction (2df)	1.000000e-05
GCST011953_3	White matter hyperintensity volume x hypertension interaction (2df)	3.000000e-06

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0006898	airway wall thickness measurement
EFO:0004314	forced expiratory volume
EFO:0004713	FEV/FVC ratio
EFO:0007828	daytime rest measurement
EFO:0004599	acute graft vs. host disease
EFO:0006501	carotid plaque build
EFO:0004343	waist-hip ratio
EFO:0005301	reading and spelling ability
EFO:0010548	xanthine measurement
EFO:0005665	white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

12 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs12630569	Efficacy	3	duloxetine	Major Depressive Disorder
rs13093500	Efficacy	3	duloxetine	Major Depressive Disorder
rs4261893	Efficacy	3	duloxetine	Major Depressive Disorder
rs4334661	Efficacy	3	duloxetine	Major Depressive Disorder
rs7616119	Efficacy	3	duloxetine	Major Depressive Disorder
rs7653345	Efficacy	3	duloxetine	Major Depressive Disorder
rs9310657	Efficacy	3	duloxetine	Major Depressive Disorder
rs9310658	Efficacy	3	duloxetine	Major Depressive Disorder
rs9819548	Efficacy	3	duloxetine	Major Depressive Disorder
rs9824595	Efficacy	3	duloxetine	Major Depressive Disorder
rs9873889	Efficacy	3	duloxetine	Major Depressive Disorder
rs9879065	Efficacy	3	duloxetine	Major Depressive Disorder

PharmGKB variants

12 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs13093500	ZNF385D	3	0.00	1	duloxetine
rs4261893	ZNF385D	3	3.00	1	duloxetine
rs4334661	ZNF385D	3	0.00	1	duloxetine
rs7616119	ZNF385D	3	0.00	1	duloxetine
rs7653345	ZNF385D	3	0.00	1	duloxetine
rs9310657	ZNF385D	3	0.00	1	duloxetine
rs9310658	ZNF385D	3	0.00	1	duloxetine
rs9819548	ZNF385D	3	0.00	1	duloxetine
rs9824595	ZNF385D	3	0.00	1	duloxetine
rs9873889	ZNF385D	3	0.00	1	duloxetine
rs9879065	ZNF385D	3	0.00	1	duloxetine
rs12630569	ZNF385D	3	0.00	1	duloxetine

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, decreases expression, affects expression	8
trichostatin A	affects cotreatment, decreases expression	3
arsenite	affects binding, increases reaction, decreases methylation	2
mercuric bromide	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Acetaminophen	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
bisphenol A	affects cotreatment, decreases methylation, increases methylation	1
dimethylselenide	decreases expression, increases oxidation	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Doxorubicin	decreases expression	1
Methamphetamine	affects response to substance	1
Phenobarbital	affects expression	1
Fenofibrate	increases expression	1
Tobacco Smoke Pollution	increases methylation	1
Tretinoin	decreases expression	1
Reactive Oxygen Species	decreases expression, increases oxidation	1
Thapsigargin	increases expression	1
Permethrin	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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