ZNF839

Summary

ZNF839 (zinc finger protein 839, HGNC:20345) is a protein-coding gene on chromosome 14q32.31, encoding Zinc finger protein 839 (A8K0R7).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 55778 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 157 total
• MANE Select transcript: NM_018335

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20345
Approved symbol	ZNF839
Name	zinc finger protein 839
Location	14q32.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000022976
Ensembl biotype	protein_coding
Entrez	55778

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 19 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000420933, ENST00000442396, ENST00000557803, ENST00000558462, ENST00000558490, ENST00000558850, ENST00000559098, ENST00000559155, ENST00000559185, ENST00000560112, ENST00000560568, ENST00000561251, ENST00000892179, ENST00000892180, ENST00000892181, ENST00000892182, ENST00000892183, ENST00000920913, ENST00000946739, ENST00000946740, ENST00000946741, ENST00000946742

RefSeq mRNA: 12 — MANE Select: NM_018335 NM_001267827, NM_001267828, NM_001385065, NM_001385069, NM_001385070, NM_001385071, NM_001385072, NM_001385073, NM_001385074, NM_001385075, NM_001385076, NM_018335

CCDS: CCDS45164, CCDS58336

Canonical transcript exons

ENST00000442396 — 8 exons

Exon	Start	End
ENSE00001743724	102331622	102331846
ENSE00001785703	102335689	102335838
ENSE00002537783	102319746	102320053
ENSE00003472446	102341323	102342367
ENSE00003583650	102325985	102326887
ENSE00003644810	102334554	102334646
ENSE00003656320	102338816	102338953
ENSE00003670069	102339094	102339223

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 90.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.6338 / max 60.4454, expressed in 1728 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
141652	6.6338	1728

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	90.23	gold quality
right testis	UBERON:0004534	90.17	gold quality
tendon of biceps brachii	UBERON:0008188	88.90	gold quality
right uterine tube	UBERON:0001302	88.49	gold quality
testis	UBERON:0000473	88.17	gold quality
muscle of leg	UBERON:0001383	85.63	gold quality
gastrocnemius	UBERON:0001388	85.33	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.26	gold quality
apex of heart	UBERON:0002098	85.17	gold quality
muscle organ	UBERON:0001630	84.89	gold quality
granulocyte	CL:0000094	84.88	gold quality
right lobe of liver	UBERON:0001114	84.22	gold quality
right lobe of thyroid gland	UBERON:0001119	83.88	gold quality
spleen	UBERON:0002106	83.46	gold quality
male germ cell	CL:0000015	83.45	gold quality
right ovary	UBERON:0002118	83.34	gold quality
sperm	CL:0000019	83.32	gold quality
vastus lateralis	UBERON:0001379	83.26	silver quality
gluteal muscle	UBERON:0002000	83.26	gold quality
quadriceps femoris	UBERON:0001377	83.01	silver quality
left ovary	UBERON:0002119	83.01	gold quality
body of pancreas	UBERON:0001150	82.99	gold quality
blood	UBERON:0000178	82.97	gold quality
skin of abdomen	UBERON:0001416	82.91	gold quality
skin of leg	UBERON:0001511	82.91	gold quality
skeletal muscle tissue	UBERON:0001134	82.89	gold quality
triceps brachii	UBERON:0001509	82.81	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.53	gold quality
right adrenal gland	UBERON:0001233	82.45	gold quality
right adrenal gland cortex	UBERON:0035827	82.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting ZNF839, 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-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6848-3P	99.64	66.49	885
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-4797-5P	99.39	68.01	1354
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-6843-3P	99.26	66.42	915
HSA-MIR-5690	99.25	67.58	1012
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-196A-3P	99.19	67.34	1204
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-371A-5P	99.08	66.51	1914
HSA-MIR-4686	98.77	66.87	964
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-518C-5P	98.53	69.20	1640
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-3187-5P	98.36	65.74	1776

Literature-anchored findings (GeneRIF, showing 1)

• ZNF839 single nucleotide polymorphism association with colorectal cancer patients survival (PMID:28138309)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf839	ENSDARG00000076988
mus_musculus	Zfp839	ENSMUSG00000021271
rattus_norvegicus	Zfp839	ENSRNOG00000031661

Protein

Protein identifiers

Zinc finger protein 839 — A8K0R7 (reviewed: A8K0R7)

Alternative names: Renal carcinoma antigen NY-REN-50

All UniProt accessions (8): A8K0R7, H0YKI3, H0YKY1, H0YLB6, H0YM06, H0YM94, H0YMU1, H0YNU6

UniProt curated annotations — full annotation on UniProt →

Isoforms (3)

UniProt ID	Names	Canonical?
A8K0R7-1	1	yes
A8K0R7-2	2
A8K0R7-5	3

RefSeq proteins (12): NP_001254756, NP_001254757, NP_001371994, NP_001371998, NP_001371999, NP_001372000, NP_001372001, NP_001372002, NP_001372003, NP_001372004, NP_001372005, NP_060805* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR031885	DUF4764	Domain
IPR039946	ZN839	Family

Pfam: PF15961

UniProt features (18 total): sequence conflict 5, sequence variant 4, region of interest 3, compositionally biased region 2, splice variant 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8K0R7-F1	50.23	0.10

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 112 (showing top): chr14q32, NUYTTEN_EZH2_TARGETS_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING, BRF1_TARGET_GENES, CHAF1B_TARGET_GENES, DYRK1A_TARGET_GENES, FOXN3_TARGET_GENES, GUCY1B1_TARGET_GENES, HOXC6_TARGET_GENES, KAT2A_TARGET_GENES, KAT5_TARGET_GENES, KLF14_TARGET_GENES, KLF7_TARGET_GENES, KMT2D_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (0):

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

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

808 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF839	WDR20	Q8TBZ3	485
ZNF839	CLBA1	Q96F83	472
ZNF839	H2AP	O75409	426
ZNF839	DCST1	Q5T197	414
ZNF839	HGD	Q93099	389
ZNF839	ZSCAN2	Q7Z7L9	385
ZNF839	STXBP6	Q8NFX7	376
ZNF839	NBPF14	Q5TI25	371
ZNF839	PFDN6	O15212	354
ZNF839	ZFYVE21	Q9BQ24	349
ZNF839	UBR7	Q8N806	346
ZNF839	SFXN3	Q9BWM7	320
ZNF839	SLC22A23	A1A5C7	307
ZNF839	ZFAND6	Q6FIF0	302
ZNF839	TRIML2	Q8N7C3	302

IntAct

5 interactions, top by confidence:

A	B	Type	Score
ZNF839	TP53	psi-mi:“MI:0915”(physical association)	0.370
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
ZNF839	YWHAE	psi-mi:“MI:0915”(physical association)	0.000
ZNF839	WNK1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (12): ZNF839 (Two-hybrid), ZNF839 (Affinity Capture-RNA), ZNF839 (Synthetic Lethality), ZNF839 (Affinity Capture-MS), ZNF839 (Affinity Capture-RNA), ZNF839 (Proximity Label-MS), ZNF839 (Co-fractionation), ZNF839 (Co-fractionation), ZNF839 (Proximity Label-MS), ZNF839 (Two-hybrid), ZNF839 (Two-hybrid), APP (Reconstituted Complex)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A1L443, A2IDD5, A5D7L8, A6NDY2, A6NIJ5, A6NNJ1, A6NNL0, A7E346, A8K0R7, A8MXJ8, A8MXZ1, B1AL46, B1ASB6, C9JSJ3, E9PGG2, O08574, P0C7V4, P0C7W8, P0C7X0, P0CG20, P0DV73, P0DV75, P0DV76, Q0VG99, Q0ZCJ7, Q149B8, Q2M3G4, Q3TQ03, Q3V0C3, Q4KLY2, Q5JXC2, Q5RCJ6, Q5SV97, Q5SW24, Q5VT03, Q5VZR2, Q6ZMY3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	113
Likely benign	28
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1709 predictions. Top by Δscore:

Variant	Effect	Δscore
14:102334550:GTA:G	acceptor_loss	1.0000
14:102334552:A:AG	acceptor_gain	1.0000
14:102334552:A:C	acceptor_loss	1.0000
14:102334553:G:GG	acceptor_gain	1.0000
14:102334643:GAAG:G	donor_gain	1.0000
14:102334647:G:GA	donor_loss	1.0000
14:102334648:TGA:T	donor_loss	1.0000
14:102334649:GAG:G	donor_loss	1.0000
14:102338814:A:AT	acceptor_loss	1.0000
14:102338815:GGTT:G	acceptor_gain	1.0000
14:102338924:G:GT	donor_gain	1.0000
14:102338945:G:T	donor_gain	1.0000
14:102338946:A:T	donor_gain	1.0000
14:102339092:A:AG	acceptor_gain	1.0000
14:102339093:G:GG	acceptor_gain	1.0000
14:102320051:CAGGT:C	donor_loss	0.9900
14:102320052:AGGTG:A	donor_loss	0.9900
14:102320054:GTGA:G	donor_loss	0.9900
14:102320055:T:A	donor_loss	0.9900
14:102331601:T:TA	acceptor_gain	0.9900
14:102331602:G:A	acceptor_gain	0.9900
14:102331844:G:GT	donor_gain	0.9900
14:102334548:T:A	acceptor_gain	0.9900
14:102334553:GTTC:G	acceptor_gain	0.9900
14:102334645:AG:A	donor_gain	0.9900
14:102334646:GG:G	donor_gain	0.9900
14:102334647:G:GG	donor_gain	0.9900
14:102335684:C:CA	acceptor_gain	0.9900
14:102338814:A:AG	acceptor_gain	0.9900
14:102338814:AG:A	acceptor_gain	0.9900

AlphaMissense

5949 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:102326667:G:A	G208E	0.998
14:102326689:T:A	H215Q	0.997
14:102326689:T:G	H215Q	0.997
14:102326476:A:C	K144N	0.996
14:102326476:A:T	K144N	0.996
14:102326492:T:C	F150L	0.996
14:102326494:C:A	F150L	0.996
14:102326494:C:G	F150L	0.996
14:102326639:T:C	C199R	0.996
14:102326660:T:C	Y206H	0.996
14:102326687:C:G	H215D	0.996
14:102326451:G:C	R136P	0.994
14:102326660:T:G	Y206D	0.994
14:102326687:C:A	H215N	0.994
14:102326441:C:A	R133S	0.993
14:102326448:G:A	G135E	0.993
14:102326656:G:C	K204N	0.993
14:102326656:G:T	K204N	0.993
14:102326667:G:T	G208V	0.993
14:102326676:G:A	G211E	0.993
14:102326685:G:C	R214P	0.993
14:102326633:T:C	F197L	0.992
14:102326635:T:A	F197L	0.992
14:102326635:T:G	F197L	0.992
14:102326639:T:A	C199S	0.992
14:102326640:G:C	C199S	0.992
14:102326654:A:G	K204E	0.992
14:102326448:G:T	G135V	0.991
14:102326466:C:A	P141H	0.991
14:102326649:G:A	C202Y	0.991

dbSNP variants (sampled 300 via entrez): RS1000094381 (14:102341375 T>C), RS1000185908 (14:102317170 A>G,T), RS1000513947 (14:102319606 C>G,T), RS1000850471 (14:102340314 C>G), RS1000950847 (14:102337647 G>A), RS1001006280 (14:102335029 A>T), RS1001205879 (14:102332024 T>C), RS1001211388 (14:102319814 G>A), RS1001357962 (14:102320203 C>A), RS1001484199 (14:102342781 C>T), RS1001671465 (14:102331778 C>G,T), RS1001697216 (14:102341292 G>A,T), RS1001781088 (14:102325635 C>T), RS1001844641 (14:102325382 G>A), RS1002011167 (14:102337998 A>G,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

5 associations (top):

Study	Trait	p-value
GCST005951_8	Body mass index	7.000000e-09
GCST006011_42	Mean corpuscular volume	2.000000e-08
GCST007656_14	Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)	1.000000e-11
GCST008476_35	Emphysema annual change measurement in smokers (percent low attenuation area)	9.000000e-06
GCST010002_161	Refractive error	1.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007626	emphysema imaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression	2
GSK-J4	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
ICG 001	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Temozolomide	increases expression	1
Leflunomide	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Methotrexate	decreases expression	1
Phthalic Acids	increases methylation	1
Selenium	affects cotreatment, decreases expression	1
Urethane	decreases expression	1
Vitamin E	affects cotreatment, decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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