ZKSCAN3

Summary

ZKSCAN3 (zinc finger with KRAB and SCAN domains 3, HGNC:13853) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger protein with KRAB and SCAN domains 3 (Q9BRR0). Transcriptional factor that binds to the consensus sequence 5’-[GT][AG][AGT]GGGG-3’ and acts as a repressor of autophagy.

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of DNA-templated transcription. Located in cytoplasm and nucleoplasm.

Source: NCBI Gene 80317 — RefSeq curated summary.

At a glance

• GWAS associations: 28
• Clinical variants (ClinVar): 64 total
• MANE Select transcript: NM_024493

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13853
Approved symbol	ZKSCAN3
Name	zinc finger with KRAB and SCAN domains 3
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	Zfp47, ZF47, ZSCAN35
Ensembl gene	ENSG00000189298
Ensembl biotype	protein_coding
OMIM	612791
Entrez	80317

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000252211, ENST00000341464, ENST00000377255, ENST00000881832, ENST00000935004, ENST00000935005

RefSeq mRNA: 3 — MANE Select: NM_024493 NM_001242894, NM_001242895, NM_024493

CCDS: CCDS4650, CCDS56408

Canonical transcript exons

ENST00000252211 — 6 exons

Exon	Start	End
ENSE00001040319	28349947	28350067
ENSE00003720339	28365426	28369172
ENSE00003889261	28359525	28359988
ENSE00003891405	28363692	28363815
ENSE00003894412	28361324	28361471
ENSE00003895903	28363303	28363385

Expression profiles

Bgee: expression breadth ubiquitous, 193 present calls, max score 84.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.0753 / max 78.0778, expressed in 1643 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66633	5.0753	1643

Top tissues by expression

285 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	84.64	gold quality
sperm	CL:0000019	78.91	silver quality
hair follicle	UBERON:0002073	78.90	gold quality
endothelial cell	CL:0000115	78.77	gold quality
male germ cell	CL:0000015	78.72	silver quality
buccal mucosa cell	CL:0002336	78.17	gold quality
stromal cell of endometrium	CL:0002255	76.82	gold quality
ventricular zone	UBERON:0003053	76.41	gold quality
smooth muscle tissue	UBERON:0001135	75.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.51	gold quality
granulocyte	CL:0000094	75.43	gold quality
olfactory bulb	UBERON:0002264	75.39	gold quality
ganglionic eminence	UBERON:0004023	75.26	gold quality
adrenal tissue	UBERON:0018303	74.96	gold quality
type B pancreatic cell	CL:0000169	74.88	gold quality
cortical plate	UBERON:0005343	74.73	gold quality
islet of Langerhans	UBERON:0000006	73.34	gold quality
cervix squamous epithelium	UBERON:0006922	73.20	gold quality
embryo	UBERON:0000922	72.86	gold quality
rectum	UBERON:0001052	72.51	gold quality
tongue squamous epithelium	UBERON:0006919	72.30	gold quality
body of uterus	UBERON:0009853	72.27	gold quality
muscle layer of sigmoid colon	UBERON:0035805	71.76	gold quality
right adrenal gland cortex	UBERON:0035827	71.73	gold quality
right adrenal gland	UBERON:0001233	71.54	gold quality
ectocervix	UBERON:0012249	71.38	gold quality
lower esophagus muscularis layer	UBERON:0035833	71.19	gold quality
lower esophagus	UBERON:0013473	71.18	gold quality
germinal epithelium of ovary	UBERON:0001304	70.71	gold quality
endocervix	UBERON:0000458	70.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.86

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

3 targets.

Target	Regulation
CCND2
ITGB4
VEGFA

JASPAR motifs

Motif	Name	Family
MA1973.1	ZKSCAN3	More than 3 adjacent zinc fingers
MA1973.2	ZKSCAN3	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:23332764

miRNA regulators (miRDB)

112 targeting ZKSCAN3, 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-4262	100.00	73.26	3931
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-4525	99.94	64.38	675
HSA-MIR-5010-5P	99.94	64.11	705
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-5682	99.89	72.56	1005
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-345-3P	99.89	70.23	1421

Literature-anchored findings (GeneRIF, showing 15)

• ZKSCAN3 adds to an expanding set of encoded products contributing to the progression of colorectal cancer (PMID:18519692)
• ZKSCAN3 regulates the expression of several genes favoring tumor progression including integrin beta 4 and VEGF (PMID:18940803)
• ZKSCAN3 induction represents a mechanism by which myeloma cells can induce cyclin D2 dysregulation and contribute to disease pathogenesis. (PMID:21057542)
• Suggest ZKSCAN3 as an autophagy master switch regulating the expression of a transcriptional network of genes integral to autophagy and lysosome biogenesis/function. (PMID:23434374)
• ZKSCAN3 appears to promote colorectal tumor progression and invasion. ZKSCAN3 may facilitate hepatic metastasis of CRC associated with CEA particularly in cases with CEA-producing tumor (PMID:27127149)
• These results suggest that ZKSCAN3 plays an important role in bladder cancer outgrowth (PMID:27447553)
• ZKSCAN3 plays a significant role in the progression of breast cancer (PMID:30049438)
• overexpression of ZKSCAN3 was frequently observed in gastric cancer cells and was significantly correlatedwith poorer clinical prognosis of patients with gastric cancer. (PMID:31892555)
• ZKSCAN3 counteracts cellular senescence by stabilizing heterochromatin. (PMID:32427330)
• Human ZKSCAN3 and Drosophila M1BP are functionally homologous transcription factors in autophagy regulation. (PMID:32541927)
• CHD1L augments autophagy-mediated migration of hepatocellular carcinoma through targeting ZKSCAN3. (PMID:34654797)
• Role of the Transcriptional Repressor Zinc Finger with KRAB and SCAN Domains 3 (ZKSCAN3) in Retinal Pigment Epithelial Cells. (PMID:34685484)
• Context-dependent pro- and anti-resection roles of ZKSCAN3 in the regulation of fork processing during replication stress. (PMID:35779634)
• Effect of Lacking ZKSCAN3 on Autophagy, Lysosomal Biogenesis and Senescence. (PMID:37175493)
• Expression of ZKSCAN3 protein suppresses proliferation, migration, and invasion of pancreatic cancer through autophagy. (PMID:38671550)

Cross-species orthologs

0 orthologs

Paralogs (30): ZNF263 (ENSG00000006194), ZNF213 (ENSG00000085644), ZNF500 (ENSG00000103199), ZKSCAN1 (ENSG00000106261), ZNF205 (ENSG00000122386), ZSCAN9 (ENSG00000137185), PGBD1 (ENSG00000137338), ZNF215 (ENSG00000149054), ZSCAN12 (ENSG00000158691), ZNF394 (ENSG00000160908), ZNF75A (ENSG00000162086), ZSCAN21 (ENSG00000166529), ZNF232 (ENSG00000167840), ZNF24 (ENSG00000172466), ZNF449 (ENSG00000173275), ZSCAN4 (ENSG00000180532), ZSCAN22 (ENSG00000182318), ZNF75D (ENSG00000186376), ZNF396 (ENSG00000186496), ZNF397 (ENSG00000186812), ZSCAN30 (ENSG00000186814), ZKSCAN4 (ENSG00000187626), ZSCAN23 (ENSG00000187987), ZSCAN16 (ENSG00000196812), ZSCAN25 (ENSG00000197037), ZSCAN26 (ENSG00000197062), ZNF165 (ENSG00000197279), ZKSCAN8 (ENSG00000198315), ZSCAN31 (ENSG00000235109), ZNF853 (ENSG00000236609)

Protein

Protein identifiers

Zinc finger protein with KRAB and SCAN domains 3 — Q9BRR0 (reviewed: Q9BRR0)

Alternative names: Zinc finger and SCAN domain-containing protein 13, Zinc finger protein 306, Zinc finger protein 309, Zinc finger protein 47 homolog

All UniProt accessions (1): Q9BRR0

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional factor that binds to the consensus sequence 5’-[GT][AG][AGT]GGGG-3’ and acts as a repressor of autophagy. Specifically represses expression of genes involved in autophagy and lysosome biogenesis/function such as MAP1LC3B, ULK1 or WIPI2. Associates with chromatin at the ITGB4 and VEGF promoters. Also acts as a transcription activator and promotes cancer cell progression and/or migration in various tumors and myelomas.

Subcellular location. Nucleus. Cytoplasm.

Induction. Overexpressed in various tumors, such as multiple myeloma, colorectal and prostate cancers (at protein level).

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

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BRR0-1	1	yes
Q9BRR0-2	2

RefSeq proteins (3): NP_001229823, NP_001229824, NP_077819* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003309	SCAN_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily

Pfam: PF00096, PF01352, PF02023

UniProt features (30 total): sequence variant 8, zinc finger region 7, sequence conflict 4, modified residue 3, domain 2, compositionally biased region 2, chain 1, region of interest 1, cross-link 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRR0-F1	60.16	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 42, 207, 449, 171

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 164 (showing top): MORF_RAGE, GOBP_REGULATION_OF_AUTOPHAGY, MORF_FLT1, GOBP_VACUOLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MORF_ESR1, GOBP_CELLULAR_SENESCENCE, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GTGCCTT_MIR506, GOBP_NEGATIVE_REGULATION_OF_AUTOPHAGY, GOBP_REGULATION_OF_CATABOLIC_PROCESS, MORF_FANCG, CAR_MLANA, LYF1_01

GO Biological Process (9): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), autophagy (GO:0006914), lysosome organization (GO:0007040), negative regulation of autophagy (GO:0010507), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), negative regulation of cellular senescence (GO:2000773), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (11): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), DNA binding (GO:0003677), chromatin binding (GO:0003682), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737)

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	4
DNA-templated transcription	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
regulation of transcription by RNA polymerase II	2
transcription by RNA polymerase II	2
binding	2
cellular anatomical structure	2
negative regulation of DNA-templated transcription	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
lytic vacuole organization	1
autophagy	1
negative regulation of catabolic process	1
regulation of autophagy	1
negative regulation of RNA biosynthetic process	1
positive regulation of RNA biosynthetic process	1
negative regulation of cellular process	1
cellular senescence	1
regulation of cellular senescence	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
DNA binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

854 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZKSCAN3	ITGB4	P16144	830
ZKSCAN3	TFEB	P19484	667
ZKSCAN3	LAMB3	Q13751	581
ZKSCAN3	ITGA6	P23229	498
ZKSCAN3	PLAUR	Q03405	497
ZKSCAN3	RAC2	P15153	491
ZKSCAN3	CCDC38	Q502W7	480
ZKSCAN3	TFE3	P19532	471
ZKSCAN3	SPATA9	Q9BWV2	444
ZKSCAN3	NKAPL	Q5M9Q1	437
ZKSCAN3	ARMC2	Q8NEN0	422
ZKSCAN3	WIPI2	Q9Y4P8	397
ZKSCAN3	MCOLN1	Q9GZU1	376
ZKSCAN3	BECN1	Q14457	357
ZKSCAN3	LRMDA	Q9H2I8	355

IntAct

88 interactions, top by confidence:

A	B	Type	Score
ZKSCAN4	SCAND1	psi-mi:“MI:0914”(association)	0.870
ZNF396	ZNF24	psi-mi:“MI:0914”(association)	0.700
LZTS2	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	LZTS2	psi-mi:“MI:0915”(physical association)	0.560
PDE4DIP	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
MEOX2	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
IHO1	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
SCAND1	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
MDM4	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3		psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	EIF2S3	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	FKBP1A	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	GFAP	psi-mi:“MI:0915”(physical association)	0.560
HSPA2	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	PMP22	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	SARS1	psi-mi:“MI:0915”(physical association)	0.560
ZKSCAN3	JPH3	psi-mi:“MI:0915”(physical association)	0.560
HTT	ZKSCAN3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (45): LZTS2 (Two-hybrid), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS), ZKSCAN3 (Affinity Capture-MS)

ESM2 similar proteins: A1YEQ3, A1YEV9, A1YFW6, A1YG26, A1YG48, A1YG60, A2T6W2, A2T712, A2T736, A2T7L7, A6QNZ0, O14978, O15535, O95125, P17022, P17029, P49910, P51815, P59923, Q07231, Q15776, Q16670, Q1LZ87, Q3MJ62, Q3URR7, Q4KLI1, Q4R8H9, Q53GI3, Q5R670, Q5R741, Q5RJ54, Q63HK3, Q642B9, Q6P9G9, Q810A1, Q86W11, Q8BGS3, Q8CF60, Q8NF99, Q92670

Diamond homologs: A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A1YGK6, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F2, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040, P28698, P49910, P51815, P59923

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1345 predictions. Top by Δscore:

Variant	Effect	Δscore
6:28350864:GCTT:G	donor_gain	1.0000
6:28353856:ACTT:A	donor_loss	0.9900
6:28353857:CTT:C	donor_loss	0.9900
6:28353858:TTA:T	donor_loss	0.9900
6:28353859:TA:T	donor_loss	0.9900
6:28353860:A:AC	donor_gain	0.9900
6:28353860:ACCAC:A	donor_loss	0.9900
6:28353861:C:CC	donor_gain	0.9900
6:28353861:CCA:C	donor_gain	0.9900
6:28353861:CCACT:C	donor_gain	0.9900
6:28359898:C:G	donor_gain	0.9900
6:28359932:G:GT	donor_gain	0.9900
6:28359936:T:TA	donor_gain	0.9900
6:28359937:G:GA	donor_gain	0.9900
6:28363301:A:AG	acceptor_gain	0.9900
6:28363302:G:GG	acceptor_gain	0.9900
6:28363690:AGG:A	acceptor_gain	0.9900
6:28363691:GGG:G	acceptor_gain	0.9900
6:28353859:TACC:T	donor_gain	0.9800
6:28353860:AC:A	donor_gain	0.9800
6:28353860:ACCA:A	donor_gain	0.9800
6:28353861:CC:C	donor_gain	0.9800
6:28353861:CCAC:C	donor_gain	0.9800
6:28358546:ATT:A	donor_gain	0.9800
6:28360600:T:G	acceptor_gain	0.9800
6:28363302:GTT:G	acceptor_gain	0.9800
6:28349965:G:GG	donor_gain	0.9700
6:28361322:AG:A	acceptor_gain	0.9700
6:28361323:GG:G	acceptor_gain	0.9700
6:28363301:A:G	acceptor_loss	0.9700

AlphaMissense

3554 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:28365719:T:C	F351L	0.999
6:28365721:C:A	F351L	0.999
6:28365721:C:G	F351L	0.999
6:28365803:T:C	F379L	0.999
6:28365805:C:A	F379L	0.999
6:28365805:C:G	F379L	0.999
6:28365887:T:C	F407L	0.999
6:28365889:C:A	F407L	0.999
6:28365889:C:G	F407L	0.999
6:28366217:T:C	F517L	0.999
6:28366219:C:A	F517L	0.999
6:28366219:C:G	F517L	0.999
6:28365971:T:C	F435L	0.998
6:28365973:T:A	F435L	0.998
6:28365973:T:G	F435L	0.998
6:28365635:T:C	F323L	0.997
6:28365637:T:A	F323L	0.997
6:28365637:T:G	F323L	0.997
6:28365720:T:C	F351S	0.997
6:28365822:T:C	L385P	0.997
6:28365832:T:A	H388Q	0.997
6:28365832:T:G	H388Q	0.997
6:28365804:T:C	F379S	0.996
6:28365830:C:G	H388D	0.996
6:28365916:T:A	H416Q	0.996
6:28365916:T:G	H416Q	0.996
6:28365746:C:G	H360D	0.995
6:28365834:A:C	Q389P	0.995
6:28365844:C:A	H392Q	0.995
6:28365844:C:G	H392Q	0.995

dbSNP variants (sampled 300 via entrez): RS1000004872 (6:28362057 T>C), RS1000075038 (6:28360102 C>G), RS1000103709 (6:28354337 G>A), RS1000320537 (6:28368532 G>C), RS1000639054 (6:28362429 G>T), RS1001358388 (6:28361683 A>G), RS1001504420 (6:28356306 T>C), RS1001555425 (6:28348272 A>G), RS1001681080 (6:28354299 T>C), RS1001786016 (6:28356018 C>T), RS1001864722 (6:28362060 C>A,T), RS1001943273 (6:28350460 G>C), RS1001964019 (6:28354064 C>T), RS1002086647 (6:28363735 A>C), RS1002272697 (6:28369168 CTTTG>C)

Disease associations

OMIM: gene MIM:612791 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

28 associations (top):

Study	Trait	p-value
GCST001251_11	Pulmonary function	2.000000e-10
GCST004183_21	Lung function (FEV1)	6.000000e-14
GCST004184_7	Lung function (FVC)	5.000000e-10
GCST004185_48	Lung function (FEV1/FVC)	4.000000e-10
GCST004521_112	Autism spectrum disorder or schizophrenia	3.000000e-26
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_212	Autism spectrum disorder or schizophrenia	5.000000e-14
GCST004521_23	Autism spectrum disorder or schizophrenia	2.000000e-11
GCST004521_43	Autism spectrum disorder or schizophrenia	2.000000e-27
GCST004521_7	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST004521_77	Autism spectrum disorder or schizophrenia	1.000000e-19
GCST004946_75	Schizophrenia	5.000000e-36
GCST005541_3	Sarcoidosis (Lofgren’s syndrome vs non-Lofgren’s syndrome)	5.000000e-18
GCST007559_16	Sleep duration (short sleep)	4.000000e-09
GCST008662_6	Lung function in never smokers (low FEV1 vs high FEV1)	1.000000e-08
GCST008921_4	Asthma and major depressive disorder	2.000000e-11
GCST009600_116	Anorexia nervosa, attention-deficit/hyperactivity disorder, autism spectrum disorder, bipolar disorder, major depression, obsessive-compulsive disorder, schizophrenia, or Tourette syndrome (pleiotropy)	1.000000e-27
GCST010002_50	Refractive error	4.000000e-34
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST012227_230	Hip circumference adjusted for BMI	4.000000e-10

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0003892	pulmonary function measurement
EFO:0004314	forced expiratory volume
EFO:0004312	vital capacity
EFO:0004713	FEV/FVC ratio
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
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

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	6
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, affects methylation, decreases methylation	1
trichostatin A	decreases expression	1
vanadyl sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	decreases expression, affects cotreatment	1
Temozolomide	increases expression	1
Fulvestrant	affects methylation, affects cotreatment	1
Fluorouracil	decreases response to substance	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Methotrexate	increases expression	1
Nickel	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D5Y9	HyCyte HeLa KO-hZKSCAN3	Cancer cell line	Female

Clinical trials (associated diseases)

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