ZFP41

Summary

ZFP41 (ZFP41 zinc finger protein, HGNC:26786) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger protein 41 homolog (Q8N8Y5). A putative DNA-binding regulatory protein associated with meiosis in spermatogenesis.

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 286128 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 57 total
• MANE Select transcript: NM_173832

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26786
Approved symbol	ZFP41
Name	ZFP41 zinc finger protein
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38705, FLJ00028, ZNF753
Ensembl gene	ENSG00000181638
Ensembl biotype	protein_coding
Entrez	286128

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000330701, ENST00000517702, ENST00000520584, ENST00000522233, ENST00000883739, ENST00000883740, ENST00000883741, ENST00000883742

RefSeq mRNA: 2 — MANE Select: NM_173832 NM_001271156, NM_173832

CCDS: CCDS6397

Canonical transcript exons

ENST00000330701 — 3 exons

Exon	Start	End
ENSE00001520791	143259775	143262705
ENSE00002090429	143246939	143247142
ENSE00003661488	143249690	143251340

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 89.19.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2247 / max 68.7528, expressed in 1729 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91394	7.2247	1729

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	89.19	gold quality
sural nerve	UBERON:0015488	82.68	gold quality
sperm	CL:0000019	81.33	silver quality
stromal cell of endometrium	CL:0002255	80.11	gold quality
cortical plate	UBERON:0005343	78.56	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.14	silver quality
hypothalamus	UBERON:0001898	77.97	gold quality
ventricular zone	UBERON:0003053	77.90	gold quality
anterior cingulate cortex	UBERON:0009835	77.80	gold quality
right frontal lobe	UBERON:0002810	77.75	gold quality
islet of Langerhans	UBERON:0000006	77.59	gold quality
tibia	UBERON:0000979	77.17	gold quality
prefrontal cortex	UBERON:0000451	76.91	gold quality
apex of heart	UBERON:0002098	76.82	gold quality
granulocyte	CL:0000094	76.81	gold quality
primary visual cortex	UBERON:0002436	76.57	gold quality
neocortex	UBERON:0001950	76.40	gold quality
lower esophagus muscularis layer	UBERON:0035833	76.26	gold quality
lower esophagus	UBERON:0013473	76.25	gold quality
amygdala	UBERON:0001876	76.15	gold quality
frontal cortex	UBERON:0001870	75.97	gold quality
Brodmann (1909) area 23	UBERON:0013554	75.95	silver quality
left ovary	UBERON:0002119	75.70	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.64	gold quality
ganglionic eminence	UBERON:0004023	75.57	gold quality
right ovary	UBERON:0002118	75.53	gold quality
body of uterus	UBERON:0009853	75.47	gold quality
cerebral cortex	UBERON:0000956	75.42	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	75.31	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting ZFP41, 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-513A-5P	100.00	69.77	2465
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554

Literature-anchored findings (GeneRIF, showing 1)

• Combining a glycolysis-related prognostic model based on scRNA-Seq with experimental verification identifies ZFP41 as a potential prognostic biomarker for HCC. (PMID:38516783)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-210j14.3	ENSDARG00000089883
danio_rerio	si:dkey-210j14.4	ENSDARG00000090871
danio_rerio	si:ch211-284e13.5	ENSDARG00000094725
danio_rerio	si:ch1073-224n8.1	ENSDARG00000104485
danio_rerio	znf16l	ENSDARG00000105532
mus_musculus	Zfp41	ENSMUSG00000047003
rattus_norvegicus	Zfp41	ENSRNOG00000007489

Paralogs (18): ZNF430 (ENSG00000118620), ZNF92 (ENSG00000146757), ZNF66 (ENSG00000160229), ZNF22 (ENSG00000165512), ZNF680 (ENSG00000173041), ZNF114 (ENSG00000178150), ZNF730 (ENSG00000183850), ZNF479 (ENSG00000185177), ZNF626 (ENSG00000188171), ZNF431 (ENSG00000196705), ZNF100 (ENSG00000197020), ZNF257 (ENSG00000197134), ZNF98 (ENSG00000197360), ZNF675 (ENSG00000197372), ZNF273 (ENSG00000198039), ZNF737 (ENSG00000237440), ZNF253 (ENSG00000256771), ZNF723 (ENSG00000268696)

Protein

Protein identifiers

Zinc finger protein 41 homolog — Q8N8Y5 (reviewed: Q8N8Y5)

All UniProt accessions (1): Q8N8Y5

UniProt curated annotations — full annotation on UniProt →

Function. A putative DNA-binding regulatory protein associated with meiosis in spermatogenesis.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

RefSeq proteins (2): NP_001258085, NP_776193* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13894

UniProt features (8 total): zinc finger region 4, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8Y5-F1	69.62	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): MODULE_255, MODULE_317, GOBP_MALE_GAMETE_GENERATION, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, MODULE_342, MODULE_69, NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP, chr8q24, MODULE_37, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE14415_ACT_VS_CTRL_NATURAL_TREG_UP, CEBPZ_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), 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
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
developmental process involved in reproduction	1
male gamete generation	1
cellular developmental process	1
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

624 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFP41	C16orf87	Q6PH81	446
ZFP41	WFDC6	Q9BQY6	419
ZFP41	BTBD19	C9JJ37	370
ZFP41	ZNF428	Q96B54	358
ZFP41	FAM90A1	Q86YD7	358
ZFP41	HCFC1R1	Q9NWW0	348
ZFP41	TEX13C	A0A0J9YWL9	348
ZFP41	ANGEL2	Q5VTE6	322
ZFP41	RBM34	P42696	320
ZFP41	GON4L	Q3T8J9	276
ZFP41	SCGB1D1	O95968	270
ZFP41	TMEM204	Q9BSN7	270
ZFP41	CREBL2	O60519	257
ZFP41	TTYH3	Q9C0H2	253
ZFP41	FIGNL1	Q6PIW4	253

IntAct

27 interactions, top by confidence:

A	B	Type	Score
ZFP41		psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZFP41	psi-mi:“MI:0915”(physical association)	0.560
ZFP41	ZNF485	psi-mi:“MI:0915”(physical association)	0.560
ZFP91	ZFP41	psi-mi:“MI:0915”(physical association)	0.560
ZFP41	LLPH	psi-mi:“MI:0915”(physical association)	0.560
ZFP41	UBL5	psi-mi:“MI:0915”(physical association)	0.560
ZFP41	SINHCAF	psi-mi:“MI:0915”(physical association)	0.560
MFAP1	ZFP41	psi-mi:“MI:0915”(physical association)	0.560
ZFP41	LRP4	psi-mi:“MI:0914”(association)	0.530
ZFP41	AGRN	psi-mi:“MI:0914”(association)	0.350
ZFP41	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.000
ZFP41	ZNF485	psi-mi:“MI:0915”(physical association)	0.000
ZFP91	ZFP41	psi-mi:“MI:0915”(physical association)	0.000
UBL5	ZFP41	psi-mi:“MI:0915”(physical association)	0.000
ZFP41	SINHCAF	psi-mi:“MI:0915”(physical association)	0.000
ZFP41	LLPH	psi-mi:“MI:0915”(physical association)	0.000
MFAP1	ZFP41	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (129): ZC3H4 (Affinity Capture-MS), MRTO4 (Affinity Capture-MS), PYGB (Affinity Capture-MS), PYGL (Affinity Capture-MS), LRP2 (Affinity Capture-MS), LRP1B (Affinity Capture-MS), LRP1 (Affinity Capture-MS), LIMA1 (Affinity Capture-MS), SAFB (Affinity Capture-MS), SAFB2 (Affinity Capture-MS), NOTCH2 (Affinity Capture-MS), RAI14 (Affinity Capture-MS), NELL2 (Affinity Capture-MS), GYS1 (Affinity Capture-MS), SORL1 (Affinity Capture-MS)

ESM2 similar proteins: D3ZUU2, E9Q8T2, G5E8B9, O08954, O35739, O95625, P07665, P10074, P19382, P22227, P25066, P25456, P38621, Q02085, Q02526, Q1H9T6, Q20082, Q3KNW1, Q3MHQ4, Q4VBD9, Q5R633, Q5SVQ8, Q62396, Q65XX7, Q68H95, Q6P2A1, Q7PN68, Q7TS63, Q811F1, Q84MZ4, Q8BIQ3, Q8N8Y5, Q8SW43, Q8T053, Q90625, Q91924, Q95RQ8, Q96C28, Q96MM3, Q99KE8

Diamond homologs: O88553, P0CG23, P17141, P21506, Q02526, Q3ZCX4, Q6ZSS3, Q8N8Y5, Q9UDV6, Q9Y2P0, Q9Y6Q3, P52742, Q6P1L6, A0A9P4XV22, A3KN32, E9Q6W4, O15391, O57311, O62836, O75820, O95863, P08048, P15822, P17010, P17012, P22227, P25490, P28698, P31509, P80944, Q00899, Q01800, Q02026, Q03172, Q0IHB8, Q0VAW7, Q0VCC5, Q29419, Q32NK7, Q3B7M4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1139 predictions. Top by Δscore:

Variant	Effect	Δscore
8:143246915:G:GT	donor_gain	0.9900
8:143247234:G:T	donor_gain	0.9900
8:143247329:A:T	donor_gain	0.9900
8:143249688:A:AG	acceptor_gain	0.9900
8:143249689:G:GG	acceptor_gain	0.9900
8:143246896:GCTCC:G	donor_gain	0.9800
8:143255405:GTT:G	donor_gain	0.9800
8:143247250:GCTT:G	donor_gain	0.9700
8:143256997:G:GT	donor_gain	0.9700
8:143257028:A:G	donor_gain	0.9700
8:143246920:G:T	donor_gain	0.9600
8:143249689:GC:G	acceptor_gain	0.9600
8:143249685:CCCAG:C	acceptor_loss	0.9400
8:143249686:CCA:C	acceptor_loss	0.9400
8:143249687:CA:C	acceptor_loss	0.9400
8:143249688:A:C	acceptor_loss	0.9400
8:143249689:G:T	acceptor_loss	0.9400
8:143247188:GC:G	donor_gain	0.9300
8:143247241:C:T	donor_gain	0.9300
8:143248501:A:G	donor_gain	0.9300
8:143249689:GCA:G	acceptor_gain	0.9300
8:143247138:GCCAG:G	donor_gain	0.9200
8:143246916:A:T	donor_gain	0.9100
8:143247180:G:GT	donor_gain	0.9000
8:143247234:G:GT	donor_gain	0.9000
8:143248445:G:GG	donor_gain	0.9000
8:143246954:C:G	donor_gain	0.8900
8:143248444:A:AG	donor_gain	0.8900
8:143247328:G:GT	donor_gain	0.8800
8:143246922:C:T	donor_gain	0.8700

AlphaMissense

1328 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:143250297:T:C	F152L	0.999
8:143250299:T:A	F152L	0.999
8:143250299:T:G	F152L	0.999
8:143250381:T:C	F180L	0.999
8:143250383:T:A	F180L	0.999
8:143250383:T:G	F180L	0.999
8:143250213:T:C	F124L	0.998
8:143250215:C:A	F124L	0.998
8:143250215:C:G	F124L	0.998
8:143250254:C:A	H137Q	0.996
8:143250254:C:G	H137Q	0.996
8:143250326:T:A	H161Q	0.996
8:143250326:T:G	H161Q	0.996
8:143250328:A:C	Q162P	0.996
8:143250129:T:C	F96L	0.995
8:143250131:T:A	F96L	0.995
8:143250131:T:G	F96L	0.995
8:143250160:A:C	Q106P	0.995
8:143250242:C:A	H133Q	0.995
8:143250242:C:G	H133Q	0.995
8:143250338:C:A	H165Q	0.995
8:143250338:C:G	H165Q	0.995
8:143250154:G:C	R104P	0.994
8:143250158:T:A	H105Q	0.994
8:143250158:T:G	H105Q	0.994
8:143250170:C:A	H109Q	0.994
8:143250170:C:G	H109Q	0.994
8:143250297:T:A	F152I	0.994
8:143250381:T:A	F180I	0.994
8:143250214:T:C	F124S	0.993

dbSNP variants (sampled 300 via entrez): RS1000127547 (8:143248826 T>A), RS1000283836 (8:143258012 A>G,T), RS1000313555 (8:143252262 G>A), RS1000354130 (8:143248212 G>A), RS1000580424 (8:143252485 G>A), RS1000657695 (8:143246491 T>G), RS1000827676 (8:143247010 A>C,G), RS1000861294 (8:143261064 G>A), RS1000949631 (8:143247350 G>T), RS1001058873 (8:143261279 G>A), RS1001093006 (8:143247162 C>G,T), RS1001148311 (8:143252122 G>C), RS1001275705 (8:143259144 G>A), RS1001306173 (8:143249418 G>A), RS1001441449 (8:143249194 T>G)

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

10 associations (top):

Study	Trait	p-value
GCST008070_105	HDL cholesterol levels	2.000000e-06
GCST008070_26	HDL cholesterol levels	2.000000e-10
GCST008075_115	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	7.000000e-16
GCST008075_61	HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)	9.000000e-12
GCST008084_21	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	8.000000e-13
GCST008084_231	HDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)	8.000000e-18
GCST008085_156	HDL cholesterol levels in current drinkers	2.000000e-09
GCST008085_24	HDL cholesterol levels in current drinkers	1.000000e-12
GCST012227_45	Hip circumference adjusted for BMI	8.000000e-09
GCST012227_46	Hip circumference adjusted for BMI	1.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0004329	alcohol drinking
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases expression, increases methylation	4
Air Pollutants	affects expression, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
manganese chloride	increases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
perfluorooctane sulfonic acid	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
bisphenol S	increases methylation	1
Arsenic	affects methylation	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation	1
Manganese	increases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	increases expression	1
Oxygen	increases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HD06	HEK293 eGFP-ZFP41	Transformed cell line	Female

Clinical trials (associated diseases)

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