ZNF613

Summary

ZNF613 (zinc finger protein 613, HGNC:25827) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 613 (Q6PF04). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 79898 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_001031721

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25827
Approved symbol	ZNF613
Name	zinc finger protein 613
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13590
Ensembl gene	ENSG00000176024
Ensembl biotype	protein_coding
Entrez	79898

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 25 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000293471, ENST00000391794, ENST00000593379, ENST00000593395, ENST00000599683, ENST00000600853, ENST00000601794, ENST00000866494, ENST00000866495, ENST00000866496, ENST00000866497, ENST00000866498, ENST00000866499, ENST00000911548, ENST00000911549, ENST00000911550, ENST00000911551, ENST00000911552, ENST00000911553, ENST00000911554, ENST00000911555, ENST00000911556, ENST00000911557, ENST00000946116, ENST00000946117, ENST00000946118, ENST00000946119

RefSeq mRNA: 2 — MANE Select: NM_001031721 NM_001031721, NM_024840

CCDS: CCDS12844, CCDS33089

Canonical transcript exons

ENST00000293471 — 6 exons

Exon	Start	End
ENSE00001365602	51929732	51929896
ENSE00001774682	51936028	51936235
ENSE00003203860	51927472	51927540
ENSE00003508621	51940617	51940709
ENSE00003553135	51940209	51940335
ENSE00003716508	51944119	51946621

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 84.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.7339 / max 28.7072, expressed in 1032 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177279	1.7339	1032

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.43	gold quality
ventricular zone	UBERON:0003053	78.95	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.73	gold quality
ganglionic eminence	UBERON:0004023	78.01	gold quality
cortical plate	UBERON:0005343	77.81	gold quality
sural nerve	UBERON:0015488	76.71	gold quality
granulocyte	CL:0000094	76.61	gold quality
islet of Langerhans	UBERON:0000006	75.94	gold quality
calcaneal tendon	UBERON:0003701	75.80	gold quality
stromal cell of endometrium	CL:0002255	75.47	gold quality
apex of heart	UBERON:0002098	75.28	gold quality
prostate gland	UBERON:0002367	75.21	gold quality
rectum	UBERON:0001052	74.94	gold quality
popliteal artery	UBERON:0002250	74.47	gold quality
tibial artery	UBERON:0007610	74.47	gold quality
descending thoracic aorta	UBERON:0002345	74.42	gold quality
right adrenal gland cortex	UBERON:0035827	74.29	gold quality
right adrenal gland	UBERON:0001233	74.28	gold quality
adrenal tissue	UBERON:0018303	74.17	gold quality
mucosa of transverse colon	UBERON:0004991	73.81	gold quality
muscle layer of sigmoid colon	UBERON:0035805	73.71	gold quality
lower esophagus muscularis layer	UBERON:0035833	73.49	gold quality
lower esophagus	UBERON:0013473	73.47	gold quality
aorta	UBERON:0000947	73.43	gold quality
left coronary artery	UBERON:0001626	73.09	gold quality
left adrenal gland	UBERON:0001234	73.01	gold quality
right coronary artery	UBERON:0001625	72.92	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	72.59	gold quality
thoracic aorta	UBERON:0001515	72.48	gold quality
left adrenal gland cortex	UBERON:0035825	72.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.30

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, STAT1

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG14442	FBGN0029893
drosophila_melanogaster	CG14440	FBGN0029894

Paralogs (11): IKZF2 (ENSG00000030419), ZNF821 (ENSG00000102984), ZNF639 (ENSG00000121864), IKZF4 (ENSG00000123411), ZNF382 (ENSG00000161298), IKZF3 (ENSG00000161405), IKZF1 (ENSG00000185811), ZNF567 (ENSG00000189042), ZNF649 (ENSG00000198093), ZNF564 (ENSG00000249709), ZNF350 (ENSG00000256683)

Protein

Protein identifiers

Zinc finger protein 613 — Q6PF04 (reviewed: Q6PF04)

All UniProt accessions (4): Q6PF04, A0A1B0GUH8, M0QX19, M0R2C1

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q6PF04-1	1	yes
Q6PF04-2	2

RefSeq proteins (2): NP_001026891, NP_079116 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF01352

UniProt features (20 total): zinc finger region 12, sequence variant 5, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PF04-F1	66.56	0.17

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 32 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, PTEN_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CIITA_TARGET_GENES, ZNF274_TARGET_GENES, ZNF350_TARGET_GENES, ZNF407_TARGET_GENES, GSE11864_UNTREATED_VS_CSF1_PAM3CYS_IN_MAC_DN, MCM3_TARGET_GENES, NKX2_5_TARGET_GENES, ZNF260_TARGET_GENES, ZNF224_TARGET_GENES, THAKAR_PBMC_INACTIVATED_INFLUENZA_AGE_21_30YO_RESPONDERS_7DY_UP

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

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
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF613	C16orf86	Q6ZW13	479
ZNF613	CYSTM1	Q9H1C7	430
ZNF613	TMEM102	Q8N9M5	364
ZNF613	FBXL6	Q8N531	359
ZNF613	NPFFR2	Q9Y5X5	349
ZNF613	CDKL1	Q00532	327
ZNF613	INTS4	Q96HW7	327
ZNF613	OR10G6	Q8NH81	323
ZNF613	CTU1	Q7Z7A3	317
ZNF613	RCCD1	A6NED2	306
ZNF613	PCDHA13	Q9Y5I0	300
ZNF613	DNAH2	Q9P225	295
ZNF613	TMTC2	Q8N394	283
ZNF613	GNG10	P50151	265
ZNF613	GIMAP8	Q8ND71	264

IntAct

16 interactions, top by confidence:

A	B	Type	Score
KRTAP5-7	ZNF613	psi-mi:“MI:0915”(physical association)	0.560
ZNF613	MDFI	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	ZNF613	psi-mi:“MI:0915”(physical association)	0.560
ZNF613	CARD10	psi-mi:“MI:0915”(physical association)	0.560
FHL5	ZNF613	psi-mi:“MI:0915”(physical association)	0.560
ZNF613	KRTAP5-7	psi-mi:“MI:0915”(physical association)	0.000
ZNF613	MDFI	psi-mi:“MI:0915”(physical association)	0.000
ZNF613	MTUS2	psi-mi:“MI:0915”(physical association)	0.000
ZNF613	CARD10	psi-mi:“MI:0915”(physical association)	0.000
ZNF613	FHL5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): ZNF613 (Two-hybrid), ZNF613 (Two-hybrid), ZNF613 (Two-hybrid), ZNF613 (Two-hybrid), KRTAP5-7 (Two-hybrid), ZNF613 (Affinity Capture-MS), ZNF613 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2L7I0, A0A1L8G2K9, A0A1P8AW69, A5D979, A8K979, B3H578, B4R4H1, D3ZVU1, F4HTH8, F4HXQ7, F4I8S3, F6UH96, G3X912, O64571, P0DKJ8, P62283, P62285, P62286, P62287, P62288, P62289, P62290, P62293, P62294, Q0IGK1, Q2PS26, Q56NI9, Q5QGU6, Q60GC1, Q6DJS0, Q6DRC5, Q6NYJ3, Q6PF04, Q7ZXG4, Q8BMI4, Q8BP27, Q8CIB9, Q8IZT6, Q8N4S0, Q94F87

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	79
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

829 predictions. Top by Δscore:

Variant	Effect	Δscore
19:51940204:TACA:T	acceptor_loss	1.0000
19:51940205:ACAGG:A	acceptor_loss	1.0000
19:51940207:A:AG	acceptor_gain	1.0000
19:51940207:A:AT	acceptor_loss	1.0000
19:51940207:AG:A	acceptor_gain	1.0000
19:51940208:G:GA	acceptor_gain	1.0000
19:51940208:GG:G	acceptor_gain	1.0000
19:51940208:GGA:G	acceptor_gain	1.0000
19:51940208:GGAA:G	acceptor_gain	1.0000
19:51940208:GGAAT:G	acceptor_gain	1.0000
19:51940332:GTGG:G	donor_gain	1.0000
19:51940333:TGGGT:T	donor_loss	1.0000
19:51940334:GG:G	donor_gain	1.0000
19:51940335:GG:G	donor_gain	1.0000
19:51940335:GGT:G	donor_loss	1.0000
19:51940336:G:GC	donor_loss	1.0000
19:51940364:A:T	donor_gain	1.0000
19:51940613:ACAG:A	acceptor_gain	1.0000
19:51940614:CA:C	acceptor_loss	1.0000
19:51940615:A:AG	acceptor_gain	1.0000
19:51940615:AG:A	acceptor_gain	1.0000
19:51940616:G:GG	acceptor_gain	1.0000
19:51940616:G:T	acceptor_loss	1.0000
19:51940616:GG:G	acceptor_gain	1.0000
19:51940616:GGGT:G	acceptor_gain	1.0000
19:51940707:CAGG:C	donor_loss	1.0000
19:51940708:AGGTG:A	donor_loss	1.0000
19:51940709:GGTG:G	donor_loss	1.0000
19:51940710:G:T	donor_loss	1.0000
19:51944115:CTA:C	acceptor_loss	1.0000

AlphaMissense

4108 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:51945192:T:C	F437L	0.998
19:51945194:C:A	F437L	0.998
19:51945194:C:G	F437L	0.998
19:51945360:T:C	F493L	0.998
19:51945362:C:A	F493L	0.998
19:51945362:C:G	F493L	0.998
19:51944688:T:C	F269L	0.997
19:51944690:C:A	F269L	0.997
19:51944690:C:G	F269L	0.997
19:51945024:T:C	F381L	0.996
19:51945026:C:A	F381L	0.996
19:51945026:C:G	F381L	0.996
19:51945108:T:C	F409L	0.996
19:51945110:C:A	F409L	0.996
19:51945110:C:G	F409L	0.996
19:51945444:T:C	F521L	0.996
19:51945446:C:A	F521L	0.996
19:51945446:C:G	F521L	0.996
19:51944772:T:C	F297L	0.995
19:51944774:C:A	F297L	0.995
19:51944774:C:G	F297L	0.995
19:51944856:T:C	F325L	0.995
19:51944858:C:A	F325L	0.995
19:51944858:C:G	F325L	0.995
19:51944940:T:C	F353L	0.995
19:51944942:C:A	F353L	0.995
19:51944942:C:G	F353L	0.995
19:51945058:G:C	R392P	0.995
19:51944604:T:C	F241L	0.994
19:51944606:C:A	F241L	0.994

dbSNP variants (sampled 300 via entrez): RS1000012452 (19:51941168 G>A), RS1000263281 (19:51926070 T>A), RS1000293806 (19:51939196 C>T), RS1000453558 (19:51932455 G>T), RS1000642831 (19:51938860 G>A,C), RS1000683205 (19:51929937 A>G), RS1000726756 (19:51945636 T>C), RS1000997429 (19:51936531 C>G), RS1001297471 (19:51927165 C>G), RS1001602841 (19:51938320 G>A,T), RS1001654042 (19:51931010 A>G), RS1001695660 (19:51926500 T>C), RS1001994691 (19:51933008 T>C), RS1002058949 (19:51944599 A>G), RS1002653825 (19:51932275 C>A,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
GCST002901_1	Survival in endocrine treated breast cancer (estrogen-receptor positive)	6.000000e-07
GCST007277_24	Tourette syndrome	9.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0000714	survival time
EFO:0007613	response to endocrine therapy

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs8113308	ZNF613		0.00	0

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases abundance, increases expression	1
ferrous chloride	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Bortezomib	increases expression, increases response to substance	1
Temozolomide	increases expression	1
Arsenic	increases abundance, increases expression	1
Phthalic Acids	increases methylation	1
Valproic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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