ZNF474

Summary

ZNF474 (zinc finger protein 474, HGNC:23245) is a protein-coding gene on chromosome 5q23.2, encoding Zinc finger protein 474 (Q6S9Z5).

Predicted to enable zinc ion binding activity. Predicted to be located in membrane.

Source: NCBI Gene 133923 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_207317

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23245
Approved symbol	ZNF474
Name	zinc finger protein 474
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Aliases	4933409D10Rik, FLJ32921
Ensembl gene	ENSG00000164185
Ensembl biotype	protein_coding
Entrez	133923

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000296600, ENST00000504912, ENST00000505843, ENST00000698748, ENST00000698749, ENST00000893400

RefSeq mRNA: 1 — MANE Select: NM_207317 NM_207317

CCDS: CCDS4130

Canonical transcript exons

ENST00000296600 — 2 exons

Exon	Start	End
ENSE00001082206	122151779	122153569
ENSE00001260890	122129546	122129683

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 92.35.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3077 / max 27.0651, expressed in 114 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58200	0.1904	74
58201	0.0981	39
58199	0.0192	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.35	gold quality
bronchial epithelial cell	CL:0002328	90.96	gold quality
bronchus	UBERON:0002185	89.35	gold quality
right uterine tube	UBERON:0001302	88.70	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.50	gold quality
mucosa of paranasal sinus	UBERON:0005030	86.00	gold quality
calcaneal tendon	UBERON:0003701	75.49	gold quality
stromal cell of endometrium	CL:0002255	70.75	gold quality
fallopian tube	UBERON:0003889	69.40	gold quality
oviduct epithelium	UBERON:0004804	66.08	gold quality
left testis	UBERON:0004533	65.74	gold quality
right testis	UBERON:0004534	65.37	gold quality
nasal cavity mucosa	UBERON:0001826	65.31	gold quality
tendon	UBERON:0000043	65.24	gold quality
testis	UBERON:0000473	64.72	gold quality
epithelium of nasopharynx	UBERON:0001951	60.65	silver quality
superficial temporal artery	UBERON:0001614	59.64	gold quality
tendon of biceps brachii	UBERON:0008188	59.35	silver quality
vena cava	UBERON:0004087	58.89	gold quality
caput epididymis	UBERON:0004358	58.21	gold quality
sperm	CL:0000019	57.91	silver quality
buccal mucosa cell	CL:0002336	57.69	gold quality
ventricular zone	UBERON:0003053	56.85	gold quality
nasal cavity epithelium	UBERON:0005384	56.61	silver quality
right lung	UBERON:0002167	56.37	gold quality
endometrium	UBERON:0001295	55.79	gold quality
parotid gland	UBERON:0001831	54.49	gold quality
gingival epithelium	UBERON:0001949	54.05	gold quality
trachea	UBERON:0003126	53.97	silver quality
gingiva	UBERON:0001828	53.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting ZNF474, 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-4482-3P	99.98	72.50	3147
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-520F-3P	99.82	71.32	1216
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-3975	99.62	65.97	697
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-4452	99.50	68.45	1493
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-10B-3P	99.04	66.98	988
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp474	ENSMUSG00000046886
rattus_norvegicus	Zfp474	ENSRNOG00000018724
drosophila_melanogaster	CG30460	FBGN0050460
drosophila_melanogaster	CG42675	FBGN0261561
caenorhabditis_elegans		WBGENE00044144

Paralogs (3): ZC2HC1A (ENSG00000104427), ZC2HC1B (ENSG00000118491), ZNF475 (ENSG00000250803)

Protein

Protein identifiers

Zinc finger protein 474 — Q6S9Z5 (reviewed: Q6S9Z5)

Alternative names: Testis-specific zinc finger protein

All UniProt accessions (5): A0A8V8TM77, A0A8V8TNM7, D6RCA7, D6RFM9, Q6S9Z5

RefSeq proteins (1): NP_997200* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR026319	ZC2HC1A/B-like	Family
IPR049899	Znf_C2HC_C3H	Domain

Pfam: PF13913

UniProt features (28 total): binding site 16, zinc finger region 4, region of interest 4, compositionally biased region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6S9Z5-F1	66.11	0.21

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 (16): 97; 100; 112; 116; 168; 171; 183; 187; 224; 227; 239; 243 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 56 (showing top): SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5, DODD_NASOPHARYNGEAL_CARCINOMA_DN, DELACROIX_RARG_BOUND_MEF, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_DN, FOXJ2_TARGET_GENES, SOX3_TARGET_GENES, ZNF322_TARGET_GENES, ZNF92_TARGET_GENES, MIR4482_3P, MIR4310, MIR4441, MIR6764_5P, MIR4700_5P, MIR1915_3P, MIR922

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 (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

200 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF474	ZNF202	O95125	660
ZNF474	A0A087WXU7	A0A087WXU7	478
ZNF474	K7ERI5	K7ERI5	478
ZNF474	M0R233	M0R233	478
ZNF474	M0R2Z0	M0R2Z0	478
ZNF474	V9GYS6	V9GYS6	478
ZNF474	M0R1X1	M0R1X1	476
ZNF474	M0R036	M0R036	447
ZNF474	ZNF556	Q9HAH1	447
ZNF474	ZNF555	Q8NEP9	393
ZNF474	ZBTB32	Q9Y2Y4	379
ZNF474	K7EJK4	K7EJK4	370
ZNF474	ZNF554	Q86TJ5	370
ZNF474	ZNF212	Q9UDV6	359
ZNF474	ZNF195	O14628	349

IntAct

88 interactions, top by confidence:

A	B	Type	Score
PFKFB1	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	TEKT4	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	GPATCH11	psi-mi:“MI:0915”(physical association)	0.560
TRIM23	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
UBASH3A	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	MCMBP	psi-mi:“MI:0915”(physical association)	0.560
ZIC1	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	ATP6V0D2	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	FRMD8	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	CPNE7	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	NOXA1	psi-mi:“MI:0915”(physical association)	0.560
IL16	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	KCTD7	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	CABP5	psi-mi:“MI:0915”(physical association)	0.560
PPL	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
PRKAB2	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	ABI2	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	RSPH14	psi-mi:“MI:0915”(physical association)	0.560
SEPHS1	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
GRB2	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	TCF19	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	CTNNA3	psi-mi:“MI:0915”(physical association)	0.560
C2CD6	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
GYS1	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	BANP	psi-mi:“MI:0915”(physical association)	0.560
MLH1	ZNF474	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	COMMD8	psi-mi:“MI:0915”(physical association)	0.560
ZNF474	TSR2	psi-mi:“MI:0915”(physical association)	0.560
TEKT4	ZNF474	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (44): ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid), ZNF474 (Two-hybrid)

ESM2 similar proteins: A4FUE7, A4FVJ7, A6QQM4, D3ZQL6, D4A039, O15013, P61406, Q0VBD2, Q1LVK9, Q1LXR6, Q32KN7, Q4R8T4, Q5FWM1, Q5HYM0, Q5PPV5, Q5RAK6, Q5REC0, Q5RHY1, Q5SPR8, Q5TFG8, Q5TKR9, Q68F67, Q6AYC8, Q6IE81, Q6P2L6, Q6PDK8, Q6PKG0, Q6S9Z5, Q6V5K9, Q7L590, Q7SXT7, Q7ZVP1, Q80U87, Q86US8, Q8BGT6, Q8BJH1, Q8BRB7, Q8BZ21, Q8C008, Q8CI51

Diamond homologs: A0A1B0GTH9, A6QQM4, Q4R8T4, Q6S9Z5, Q6V5K9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	3
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

2390 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:122152300:T:C	F104L	0.984
5:122152302:T:A	F104L	0.984
5:122152302:T:G	F104L	0.984
5:122152681:T:C	F231L	0.964
5:122152683:T:A	F231L	0.964
5:122152683:T:G	F231L	0.964
5:122152362:C:A	N124K	0.958
5:122152362:C:G	N124K	0.958
5:122152350:G:C	W120C	0.953
5:122152350:G:T	W120C	0.953
5:122152513:T:C	F175L	0.950
5:122152515:C:A	F175L	0.950
5:122152515:C:G	F175L	0.950
5:122152279:T:C	C97R	0.941
5:122152348:T:A	W120R	0.931
5:122152348:T:C	W120R	0.931
5:122152279:T:A	C97S	0.924
5:122152280:G:C	C97S	0.924
5:122152336:T:A	C116S	0.914
5:122152337:G:C	C116S	0.914
5:122152281:C:G	C97W	0.911
5:122152361:A:T	N124I	0.911
5:122152280:G:A	C97Y	0.905
5:122152295:G:C	R102P	0.890
5:122152336:T:C	C116R	0.883
5:122152361:A:C	N124T	0.883
5:122152660:T:C	C224R	0.883
5:122152288:T:A	C100S	0.882
5:122152289:G:C	C100S	0.882
5:122152326:T:A	H112Q	0.882

dbSNP variants (sampled 300 via entrez): RS1000094627 (5:122130181 A>T), RS1000150827 (5:122133222 A>T), RS1000162215 (5:122132917 T>C), RS1000190745 (5:122136948 A>C,G), RS1000204931 (5:122131159 G>A), RS1000639896 (5:122135974 T>C), RS1000645989 (5:122136668 T>C), RS1000695459 (5:122138466 T>C), RS1000709209 (5:122137185 G>A), RS1000754533 (5:122143550 T>C), RS1000823690 (5:122151773 C>T), RS1001038260 (5:122148438 A>G), RS1001062403 (5:122151555 G>A,C,T), RS1001093594 (5:122151377 G>T), RS1001341630 (5:122146448 C>T)

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

2 associations (top):

Study	Trait	p-value
GCST005580_17	Intraocular pressure	2.000000e-14
GCST005580_27	Intraocular pressure	6.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression	2
Air Pollutants	increases abundance, increases expression	2
Benzo(a)pyrene	increases expression, affects methylation, decreases methylation	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
butyraldehyde	decreases expression	1
perfluorooctanoic acid	decreases expression	1
abrine	increases expression	1
bisphenol S	decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
incobotulinumtoxinA	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Smoke	increases abundance, 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.