ZFAND4

Summary

ZFAND4 (zinc finger AN1-type containing 4, HGNC:23504) is a protein-coding gene on chromosome 10q11.22, encoding AN1-type zinc finger protein 4 (Q86XD8).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 93550 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 133 total
• MANE Select transcript: NM_174890

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23504
Approved symbol	ZFAND4
Name	zinc finger AN1-type containing 4
Location	10q11.22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40185
Ensembl gene	ENSG00000172671
Ensembl biotype	protein_coding
Entrez	93550

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 15 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000335258, ENST00000344646, ENST00000374366, ENST00000374370, ENST00000374371, ENST00000465407, ENST00000484333, ENST00000495747, ENST00000497028, ENST00000907319, ENST00000907320, ENST00000907321, ENST00000907322, ENST00000907323, ENST00000940115, ENST00000940116, ENST00000940117, ENST00000940118, ENST00000940119, ENST00000947494, ENST00000947495

RefSeq mRNA: 4 — MANE Select: NM_174890 NM_001128324, NM_001282905, NM_001282906, NM_174890

CCDS: CCDS60520, CCDS7214

Canonical transcript exons

ENST00000344646 — 10 exons

Exon	Start	End
ENSE00001840813	45615500	45616571
ENSE00001903929	45672250	45672772
ENSE00003494261	45639816	45639963
ENSE00003494639	45624583	45624637
ENSE00003565417	45652984	45653059
ENSE00003599980	45663542	45663842
ENSE00003620960	45618140	45618260
ENSE00003634119	45625951	45627105
ENSE00003641406	45648294	45648534
ENSE00003641592	45651966	45652033

Expression profiles

Bgee: expression breadth ubiquitous, 202 present calls, max score 97.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9845 / max 246.7435, expressed in 1568 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
109247	6.4083	1537
109246	0.4405	215
109245	0.1357	50

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.33	gold quality
left testis	UBERON:0004533	94.80	gold quality
right testis	UBERON:0004534	94.68	gold quality
testis	UBERON:0000473	93.29	gold quality
buccal mucosa cell	CL:0002336	88.29	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.84	gold quality
oviduct epithelium	UBERON:0004804	86.25	gold quality
adult organism	UBERON:0007023	85.00	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.70	gold quality
islet of Langerhans	UBERON:0000006	82.58	gold quality
calcaneal tendon	UBERON:0003701	82.43	gold quality
bone marrow cell	CL:0002092	81.79	gold quality
right lobe of liver	UBERON:0001114	81.30	gold quality
cerebellar cortex	UBERON:0002129	80.95	gold quality
cerebellar hemisphere	UBERON:0002245	80.92	gold quality
right adrenal gland cortex	UBERON:0035827	80.76	gold quality
granulocyte	CL:0000094	80.56	gold quality
leukocyte	CL:0000738	80.08	gold quality
cerebellum	UBERON:0002037	80.07	gold quality
monocyte	CL:0000576	79.98	gold quality
right hemisphere of cerebellum	UBERON:0014890	79.81	gold quality
adrenal tissue	UBERON:0018303	79.65	gold quality
right adrenal gland	UBERON:0001233	79.49	gold quality
mucosa of paranasal sinus	UBERON:0005030	79.48	gold quality
left adrenal gland cortex	UBERON:0035825	79.16	gold quality
left adrenal gland	UBERON:0001234	79.14	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.98	gold quality
colonic epithelium	UBERON:0000397	78.08	gold quality
ventricular zone	UBERON:0003053	77.91	gold quality
adrenal gland	UBERON:0002369	77.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.87

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting ZFAND4, 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-4262	100.00	73.26	3931
HSA-MIR-340-5P	100.00	72.50	4437
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-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-7-1-3P	99.91	71.53	4384

Literature-anchored findings (GeneRIF, showing 2)

• In gastric cancer cells, ANUBL1 was upregulated and promoted proliferation of SGC-7901 cells. Over-expression decreased miR-182 expression. ANUBL1 expression was in turn directly downregulated by miR-182 in a negative feedback loop. (PMID:25682742)
• Suggest that ZFAND4 is a useful marker for predicting metastasis and poor prognosis in patients with oral squamous cell carcinoma. (PMID:29074611)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfand4	ENSDARG00000076703
mus_musculus	Zfand4	ENSMUSG00000042213
rattus_norvegicus	Zfand4	ENSRNOG00000011791

Paralogs (10): UBL4A (ENSG00000102178), NEDD8 (ENSG00000129559), RPS27A (ENSG00000143947), UBC (ENSG00000150991), UBB (ENSG00000170315), UBL4B (ENSG00000186150), ISG15 (ENSG00000187608), ANKUB1 (ENSG00000206199), UBD (ENSG00000213886), UBA52 (ENSG00000221983)

Protein

Protein identifiers

AN1-type zinc finger protein 4 — Q86XD8 (reviewed: Q86XD8)

Alternative names: AN1-type zinc finger and ubiquitin domain-containing protein-like 1

All UniProt accessions (5): Q86XD8, A0A087WT56, F2Z2H4, J3KPC0, Q5VVY4

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (4): NP_001121796, NP_001269834, NP_001269835, NP_777550* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000058	Znf_AN1	Domain
IPR000626	Ubiquitin-like_dom	Domain
IPR019956	Ubiquitin_dom	Domain
IPR029071	Ubiquitin-like_domsf	Homologous_superfamily
IPR035896	AN1-like_Znf	Homologous_superfamily
IPR053061	AN1-type_zinc_finger	Family

Pfam: PF00240, PF01428

UniProt features (17 total): binding site 8, sequence variant 3, region of interest 2, chain 1, domain 1, zinc finger region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XD8-F1	53.32	0.19

Functional residue map

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

Ligand- & substrate-binding residues (8): 689; 692; 698; 700; 667; 670; 682; 684

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 136 (showing top): TGCACTT_MIR519C_MIR519B_MIR519A, TTGGAGA_MIR5155P_MIR519E, ZHANG_BREAST_CANCER_PROGENITORS_UP, THUM_SYSTOLIC_HEART_FAILURE_DN, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, OHGUCHI_LIVER_HNF4A_TARGETS_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNG_KO_UP, CIITA_TARGET_GENES, ELF2_TARGET_GENES, FEV_TARGET_GENES, ZBTB12_TARGET_GENES, ZNF274_TARGET_GENES, ZNF592_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

4200 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFAND4	LRCH1	Q9Y2L9	626
ZFAND4	C9orf43	Q8TAL5	594
ZFAND4	PKDREJ	Q9NTG1	590
ZFAND4	FAM209A	Q5JX71	590
ZFAND4	SPATA31G1	Q5VYM1	561
ZFAND4	WASHC2C	Q9Y4E1	561
ZFAND4	MAGEB16	A2A368	560
ZFAND4	UBL4B	Q8N7F7	548
ZFAND4	REDIC1	Q86WS4	545
ZFAND4	KLHL32	Q96NJ5	535
ZFAND4	TMCO5A	Q8N6Q1	531
ZFAND4	TULP2	O00295	497
ZFAND4	C3orf22	Q8N5N4	478
ZFAND4	SPATA16	Q9BXB7	475
ZFAND4	LRP10	Q7Z4F1	456

IntAct

5 interactions, top by confidence:

A	B	Type	Score
ZFAND4	A2ML1	psi-mi:“MI:0914”(association)	0.530
ZFAND4	SF3B6	psi-mi:“MI:0915”(physical association)	0.400
TFAP2C	ZFAND4	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (10): A2ML1 (Affinity Capture-MS), SERPINB4 (Affinity Capture-MS), SF3B6 (Proximity Label-MS), ZFAND4 (Proximity Label-MS), ZFAND4 (Affinity Capture-RNA), A2ML1 (Affinity Capture-MS), SERPINB4 (Affinity Capture-MS), ZFAND4 (PCA), ZFAND4 (Affinity Capture-RNA), TFAP2C (Two-hybrid)

ESM2 similar proteins: A0A087WXM9, A0A2K1JJ00, A0JM83, A4IGL8, E1BC15, E9Q5F9, O14513, O35923, O60673, O88491, P46013, P97929, Q14B71, Q28DZ0, Q29RT4, Q3MHH3, Q3TNU4, Q3ZBP0, Q4QY64, Q4V7J0, Q5DTT3, Q5E9A0, Q5F2C3, Q5RD08, Q5VWN6, Q5VYV7, Q61493, Q69YH5, Q6NS59, Q703I1, Q80U59, Q86XD8, Q8IXS0, Q8IYL3, Q8L7I1, Q8N7Z5, Q8NFU7, Q8TEP8, Q92628, Q96BU1

Diamond homologs: A2YEZ6, A2Z2J6, A3BDI8, A3C039, B5DF11, D3Z3C6, O49663, O76080, O88878, P0C282, Q0DJC7, Q3EA33, Q3SZY7, Q5JLA7, Q5JN07, Q5R7S6, Q69LE0, Q6DGF4, Q6FIF0, Q6H754, Q6H7P8, Q6NNI8, Q6Z541, Q7Y1W9, Q84PD8, Q852K5, Q852K6, Q852K8, Q86XD8, Q8H0X0, Q942F8, Q94B40, Q9DCH6, Q9H8U3, Q9LHJ8, Q9SJM6, Q9STJ9, Q9SZ69, Q9ZNU9, O18973

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	117
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2977 predictions. Top by Δscore:

Variant	Effect	Δscore
10:45618151:G:C	donor_gain	1.0000
10:45618175:T:A	donor_gain	1.0000
10:45639959:CACCA:C	acceptor_gain	1.0000
10:45639964:C:CC	acceptor_gain	1.0000
10:45641171:C:CC	acceptor_gain	1.0000
10:45648535:C:CC	acceptor_gain	1.0000
10:45652982:A:AC	donor_gain	1.0000
10:45652983:C:CC	donor_gain	1.0000
10:45672249:CACA:C	donor_gain	1.0000
10:45618080:AAT:A	donor_gain	0.9900
10:45618080:AATC:A	donor_gain	0.9900
10:45618097:A:AC	donor_gain	0.9900
10:45618117:G:C	donor_gain	0.9900
10:45618163:T:TA	donor_gain	0.9900
10:45618207:T:TA	donor_gain	0.9900
10:45618257:TCTCC:T	acceptor_loss	0.9900
10:45618258:CTC:C	acceptor_gain	0.9900
10:45618259:TCCTG:T	acceptor_loss	0.9900
10:45618261:C:A	acceptor_loss	0.9900
10:45618261:C:CC	acceptor_gain	0.9900
10:45618262:T:A	acceptor_loss	0.9900
10:45639810:CTTCA:C	donor_loss	0.9900
10:45639811:TTCA:T	donor_loss	0.9900
10:45639812:TCA:T	donor_loss	0.9900
10:45639813:CA:C	donor_loss	0.9900
10:45639814:AC:A	donor_loss	0.9900
10:45639815:CCTTT:C	donor_loss	0.9900
10:45639816:C:G	donor_loss	0.9900
10:45639846:AG:A	donor_gain	0.9900
10:45639960:ACCA:A	acceptor_gain	0.9900

AlphaMissense

4775 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:45616556:G:C	F688L	0.982
10:45616556:G:T	F688L	0.982
10:45616558:A:G	F688L	0.982
10:45653035:A:G	L70S	0.971
10:45663606:A:C	F40L	0.969
10:45663606:A:T	F40L	0.969
10:45663608:A:G	F40L	0.969
10:45618143:C:G	C682S	0.966
10:45618144:A:T	C682S	0.966
10:45653014:A:T	L77H	0.965
10:45652013:A:G	L94S	0.964
10:45616521:C:G	C700S	0.963
10:45616522:A:T	C700S	0.963
10:45616522:A:G	C700R	0.962
10:45652996:A:G	L83S	0.962
10:45652031:A:G	I88T	0.961
10:45618144:A:G	C682R	0.960
10:45653040:T:A	Q68H	0.957
10:45653040:T:G	Q68H	0.957
10:45616440:A:G	I727T	0.952
10:45639853:A:G	L227P	0.951
10:45663564:T:A	K54N	0.950
10:45663564:T:G	K54N	0.950
10:45618188:C:G	C667S	0.949
10:45618189:A:T	C667S	0.949
10:45652031:A:C	I88S	0.949
10:45618187:A:C	C667W	0.946
10:45663637:A:G	L30P	0.946
10:45616440:A:C	I727S	0.945
10:45616569:C:G	C684S	0.945

dbSNP variants (sampled 300 via entrez): RS1000057889 (10:45652022 C>G), RS1000074980 (10:45671999 G>A), RS1000151908 (10:45655675 A>T), RS1000184064 (10:45630313 G>A,C), RS1000220177 (10:45645448 T>A,C), RS1000300734 (10:45622919 A>G), RS1000355942 (10:45666578 T>C), RS1000357391 (10:45623898 A>T), RS1000411868 (10:45659899 C>T), RS1000412758 (10:45623647 G>A), RS1000422513 (10:45639916 T>C), RS1000533692 (10:45671207 T>C), RS1000537975 (10:45654359 G>A), RS1000543796 (10:45671531 T>C,G), RS1000581873 (10:45627000 T>C)

Disease associations

OMIM: gene `` | 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
GCST000585_14	Mean corpuscular volume	3.000000e-11
GCST000587_14	Mean corpuscular hemoglobin	4.000000e-12
GCST006011_78	Mean corpuscular volume	2.000000e-42
GCST90011900_47	Serum alkaline phosphatase levels	7.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004509	hemoglobin measurement
EFO:0004527	mean corpuscular hemoglobin
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Estradiol	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Vanadates	decreases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

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