ZNF475

Summary

ZNF475 (zinc finger protein 475, HGNC:53564) is a protein-coding gene on chromosome 5q23.2, encoding Zinc finger protein 475 (A0A1B0GTH9).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 100505841 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001195535

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53564
Approved symbol	ZNF475
Name	zinc finger protein 475
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000250803
Ensembl biotype	protein_coding
Entrez	100505841

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000509403, ENST00000514637, ENST00000514925, ENST00000515596, ENST00000866239

RefSeq mRNA: 1 — MANE Select: NM_001195535 NM_001195535

CCDS: CCDS93768

Canonical transcript exons

ENST00000509403 — 3 exons

Exon	Start	End
ENSE00002028099	122160176	122160262
ENSE00002033337	122182491	122182658
ENSE00002056848	122179550	122179730

Expression profiles

Bgee: expression breadth ubiquitous, 115 present calls, max score 98.28.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.28	gold quality
buccal mucosa cell	CL:0002336	96.96	gold quality
left testis	UBERON:0004533	96.62	gold quality
right testis	UBERON:0004534	96.32	gold quality
testis	UBERON:0000473	93.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.77	gold quality
adult organism	UBERON:0007023	84.81	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.70	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.59	gold quality
right uterine tube	UBERON:0001302	74.49	gold quality
cardiac muscle of right atrium	UBERON:0003379	72.37	gold quality
left ventricle myocardium	UBERON:0006566	72.26	gold quality
kidney epithelium	UBERON:0004819	70.58	gold quality
bronchial epithelial cell	CL:0002328	68.48	gold quality
bronchus	UBERON:0002185	67.21	gold quality
mucosa of paranasal sinus	UBERON:0005030	66.71	silver quality
ileal mucosa	UBERON:0000331	65.42	silver quality
epithelial cell of pancreas	CL:0000083	64.83	gold quality
tibialis anterior	UBERON:0001385	64.20	silver quality
upper arm skin	UBERON:0004263	63.33	gold quality
nasal cavity mucosa	UBERON:0001826	60.81	gold quality
oviduct epithelium	UBERON:0004804	60.51	gold quality
myocardium	UBERON:0002349	59.85	gold quality
calcaneal tendon	UBERON:0003701	59.36	gold quality
epithelium of nasopharynx	UBERON:0001951	59.21	silver quality
fallopian tube	UBERON:0003889	58.62	gold quality
deltoid	UBERON:0001476	58.56	gold quality
lateral nuclear group of thalamus	UBERON:0002736	57.98	gold quality
quadriceps femoris	UBERON:0001377	57.75	gold quality
nasal cavity epithelium	UBERON:0005384	56.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	2633.36
E-ANND-3	yes	4.85

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700034E13Rik	ENSMUSG00000024532
drosophila_melanogaster	CG30460	FBGN0050460
drosophila_melanogaster	CG42675	FBGN0261561

Paralogs (3): ZC2HC1A (ENSG00000104427), ZC2HC1B (ENSG00000118491), ZNF474 (ENSG00000164185)

Protein

Protein identifiers

Zinc finger protein 475 — A0A1B0GTH9 (reviewed: A0A1B0GTH9)

All UniProt accessions (3): A0A1B0GTH9, A0A1B0GW86, A0A1B0GWJ1

RefSeq proteins (1): NP_001182464* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF13913

UniProt features (11 total): binding site 8, zinc finger region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GTH9-F1	87.10	0.66

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): 102; 10; 13; 25; 29; 83; 86; 98

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 18 (showing top): FOXJ2_TARGET_GENES, SOX3_TARGET_GENES, ZNF322_TARGET_GENES, ZNF92_TARGET_GENES, GSE13306_TREG_VS_TCONV_DN, DESCARTES_MAIN_FETAL_CILIATED_EPITHELIAL_CELLS, DESCARTES_FETAL_LUNG_CILIATED_EPITHELIAL_CELLS, GSE32423_CTRL_VS_IL7_MEMORY_CD8_TCELL_DN, GSE8835_HEALTHY_VS_CLL_CD4_TCELL_DN, chr5q23, GSE21670_STAT3_KO_VS_WT_CD4_TCELL_TGFB_TREATED_UP, GSE21546_WT_VS_SAP1A_KO_ANTI_CD3_STIM_DP_THYMOCYTES_UP, GSE26351_WNT_VS_BMP_PATHWAY_STIM_HEMATOPOIETIC_PROGENITORS_UP, GSE29164_DAY3_VS_DAY7_CD8_TCELL_AND_IL12_TREATED_MELANOMA_DN, GSE36078_UNTREATED_VS_AD5_T425A_HEXON_INF_IL1R_KO_MOUSE_LUNG_DC_UP

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), 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
cation binding	1

Protein interactions and networks

STRING

20 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF475	C3orf70	A6NLC5	221
ZNF475	RRP7A	Q9Y3A4	219
ZNF475	SPINK14	Q6IE38	184
ZNF475	EFR3B	Q9Y2G0	162
ZNF475	YIF1B	Q5BJH7	156
ZNF475	SLC33A2	Q96ES6	143
ZNF475	SLC33A1	O00400	143
ZNF475	CFAP161	Q6P656	0
ZNF475	ZNHIT1	O43257	0
ZNF475	CFAP57	Q96MR6	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTH9, A6QQM4, A7SKE9, B4KLC0, B4LRY2, B4Q5Z1, E0X9N4, O60308, P0CR50, P0CR51, P10711, P23193, Q02336, Q09464, Q0VA16, Q15560, Q17CJ5, Q1HE00, Q28CY2, Q29RL9, Q3B7L8, Q3EA33, Q4KLL0, Q4R4J1, Q4V7D7, Q5EB92, Q5RAY5, Q5U2P3, Q5ZM16, Q63799, Q641B2, Q6DJI8, Q6DRC4, Q6GPP0, Q6IDS6, Q6NZZ9, Q6P616, Q7QJV0, Q7ZXB5, Q8BHS3

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

702 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:122182583:T:C	F90L	0.997
5:122182585:C:A	F90L	0.997
5:122182585:C:G	F90L	0.997
5:122179583:T:C	C10R	0.990
5:122182607:C:G	H98D	0.989
5:122179628:C:G	H25D	0.988
5:122179640:T:A	C29S	0.988
5:122179641:G:C	C29S	0.988
5:122179654:G:C	W33C	0.988
5:122179654:G:T	W33C	0.988
5:122182584:T:C	F90S	0.986
5:122179630:T:A	H25Q	0.985
5:122179630:T:G	H25Q	0.985
5:122179583:T:A	C10S	0.984
5:122179584:G:C	C10S	0.984
5:122179640:T:C	C29R	0.984
5:122182578:G:C	R88P	0.984
5:122182584:T:G	F90C	0.984
5:122179608:G:A	G18E	0.982
5:122179652:T:A	W33R	0.982
5:122179652:T:C	W33R	0.982
5:122182571:T:C	C86R	0.982
5:122179666:C:A	N37K	0.981
5:122179666:C:G	N37K	0.981
5:122182562:T:C	C83R	0.981
5:122182571:T:A	C86S	0.981
5:122182572:G:C	C86S	0.981
5:122179599:G:C	R15P	0.980
5:122179592:T:A	C13S	0.979
5:122179592:T:C	C13R	0.979

dbSNP variants (sampled 300 via entrez): RS1000029119 (5:122170470 C>A), RS1000031112 (5:122167852 T>A), RS1000092078 (5:122161890 T>A), RS1000193877 (5:122168201 T>A), RS1000254074 (5:122172894 A>C,G), RS1000436178 (5:122178337 T>A), RS1000466402 (5:122167507 G>A), RS1000586503 (5:122171649 C>G), RS1000677265 (5:122176705 T>A,G), RS1000848991 (5:122158959 GT>G), RS1000918351 (5:122182064 C>T), RS1000968758 (5:122181799 A>G,T), RS1001176495 (5:122178484 C>A,T), RS1001296949 (5:122181226 T>A), RS1001310886 (5:122162632 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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