ZNF292

Summary

ZNF292 (zinc finger protein 292, HGNC:18410) is a protein-coding gene on chromosome 6q14.3, encoding Zinc finger protein 292 (O60281). May be involved in transcriptional regulation.

This gene encodes a growth hormone-dependent, zinc finger transcription factor that functions as a tumor suppressor. Naturally occurring mutations in this gene are associated with gastric cancer, colorectal cancer, and chronic lymphocytic leukemia.

Source: NCBI Gene 23036 — RefSeq curated summary.

At a glance

• Gene–disease (curated): complex neurodevelopmental disorder (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 8
• Clinical variants (ClinVar): 851 total — 36 pathogenic, 59 likely-pathogenic
• Phenotypes (HPO): 40
• Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
• MANE Select transcript: NM_015021

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18410
Approved symbol	ZNF292
Name	zinc finger protein 292
Location	6q14.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16
Ensembl gene	ENSG00000188994
Ensembl biotype	protein_coding
OMIM	616213
Entrez	23036

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 9 protein_coding, 4 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000339907, ENST00000369577, ENST00000369578, ENST00000392985, ENST00000466062, ENST00000485016, ENST00000496806, ENST00000518845, ENST00000524067, ENST00000699914, ENST00000699923, ENST00000699924, ENST00000699925, ENST00000699989, ENST00000699990, ENST00000699991, ENST00000911479

RefSeq mRNA: 2 — MANE Select: NM_015021 NM_001351444, NM_015021

CCDS: CCDS47457

Canonical transcript exons

ENST00000369577 — 8 exons

Exon	Start	End
ENSE00001561553	87155565	87155759
ENSE00003977974	87245503	87245644
ENSE00003977975	87233325	87233527
ENSE00003977977	87243475	87243611
ENSE00003977978	87216299	87216377
ENSE00003977979	87218596	87218731
ENSE00003977982	87215903	87216057
ENSE00003978011	87254650	87265943

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 97.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.0566 / max 261.2606, expressed in 1758 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
68829	15.9680	1758
68833	0.0886	38

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	97.64	gold quality
calcaneal tendon	UBERON:0003701	97.49	gold quality
cauda epididymis	UBERON:0004360	97.27	gold quality
corpus epididymis	UBERON:0004359	97.25	gold quality
trabecular bone tissue	UBERON:0002483	97.14	gold quality
hair follicle	UBERON:0002073	97.10	gold quality
cranial nerve II	UBERON:0000941	96.89	gold quality
tongue squamous epithelium	UBERON:0006919	96.57	gold quality
skin of hip	UBERON:0001554	96.32	gold quality
jejunal mucosa	UBERON:0000399	95.92	gold quality
oral cavity	UBERON:0000167	95.88	gold quality
buccal mucosa cell	CL:0002336	95.46	gold quality
superficial temporal artery	UBERON:0001614	95.26	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	94.72	gold quality
cartilage tissue	UBERON:0002418	94.58	gold quality
pigmented layer of retina	UBERON:0001782	94.56	gold quality
corpus callosum	UBERON:0002336	94.53	gold quality
sural nerve	UBERON:0015488	94.51	gold quality
ganglionic eminence	UBERON:0004023	94.46	gold quality
epithelium of nasopharynx	UBERON:0001951	94.41	gold quality
lateral globus pallidus	UBERON:0002476	94.31	gold quality
ventricular zone	UBERON:0003053	94.21	gold quality
pylorus	UBERON:0001166	94.17	gold quality
mammalian vulva	UBERON:0000997	94.13	gold quality
renal medulla	UBERON:0000362	94.12	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.03	gold quality
embryo	UBERON:0000922	93.84	gold quality
superior surface of tongue	UBERON:0007371	93.80	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.72	gold quality
colonic epithelium	UBERON:0000397	93.63	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-106540	no	759.30
E-CURD-89	no	717.45
E-MTAB-7606	no	652.99
E-MTAB-6108	no	233.15
E-ANND-3	no	0.00

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
GH1	Activation

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

154 targeting ZNF292, 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-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-548AJ-3P	99.96	73.38	5345

Functional genomics

ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 6)

• ZNF292 is a new tumor-suppressor gene with potential relevance to colorectal cancer. (PMID:25559195)
• Based on this, the ZNF292 frameshift mutations may possibly contribute to tumorigenesis by altering its tumor suppressor gene functions in gastric and colorectal cancers. (PMID:27150435)
• De novo and inherited variants in ZNF292 underlie a neurodevelopmental disorder with features of autism spectrum disorder. (PMID:31723249)
• Circular RNA circZNF292 regulates H2 O2 -induced injury in human lens epithelial HLE-B3 cells depending on the regulation of the miR-222-3p/E2F3 axis. (PMID:33851769)
• Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses. (PMID:34789007)
• The role of exosomal circular RNA ZNF292 in intermittent hypoxia-induced AC16 cardiomyocytes injury. (PMID:37726500)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf292a	ENSDARG00000016763
danio_rerio	znf292b	ENSDARG00000043973
mus_musculus	Zfp292	ENSMUSG00000039967
rattus_norvegicus	Zfp292	ENSRNOG00000031031

Paralogs (2): RLF (ENSG00000117000), ZNF654 (ENSG00000175105)

Protein

Protein identifiers

Zinc finger protein 292 — O60281 (reviewed: O60281)

All UniProt accessions (9): A0A8V8TP18, A0A8V8TPC9, A0A8V8TPI9, A0A8V8TQW3, E5RJG2, O60281, H0YAU0, H0YB79, J3KNV1

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Disease relevance. Intellectual developmental disorder, autosomal dominant 64 (MRD64) [MIM:619188] An autosomal dominant form of intellectual disability, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD64 is characterized by mildly to severely impaired intellectual development, speech delay, and autism spectrum disorder in most patients. Additional variable features may include motor delay, attention deficit-hyperactivity disorder, and non-specific dysmorphic features. The disease is caused by variants affecting the gene represented in this entry.

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

Isoforms (2)

UniProt ID	Names	Canonical?
O60281-1	1	yes
O60281-2	2

RefSeq proteins (2): NP_001338373, NP_055836* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR052251	GH-ZnFinger_Regulators	Family
IPR057986	TPR_Rlf/292/654	Domain
IPR058902	Znf_C2H2_ZNF292/Rlf	Domain

Pfam: PF00096, PF25420, PF25580, PF26218

UniProt features (71 total): zinc finger region 15, sequence variant 15, compositionally biased region 12, region of interest 10, sequence conflict 8, modified residue 4, splice variant 2, strand 2, chain 1, coiled-coil region 1, helix 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7N2D	ELECTRON CRYSTALLOGRAPHY	1.5
1X3C	SOLUTION NMR

Predicted structure (AlphaFold)

No AlphaFold model available for O60281 — AlphaFold DB does not currently provide models for proteins above ~3000 aa.

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): 654, 1117, 1159, 2042

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 313 (showing top): MORF_ATRX, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MODULE_493, DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN, MODULE_171, MODULE_301, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, LIAO_METASTASIS, MORF_RAP1A, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, GCM_NF2, MORF_MT4, GCM_RBM8A

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (5): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
positive regulation of DNA-templated transcription	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
nucleic acid binding	1
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1546 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF292	C6orf163	Q5TEZ5	532
ZNF292	MED13L	Q71F56	530
ZNF292	RALGAPB	Q86X10	504
ZNF292	WDFY3	Q8IZQ1	475
ZNF292	ZNF517	Q6ZMY9	461
ZNF292	CHD8	Q9HCK8	457
ZNF292	ZNF462	Q96JM2	448
ZNF292	POGZ	Q7Z3K3	447
ZNF292	KLF7	O75840	447
ZNF292	ZNF18	P17022	447
ZNF292	ZMYM3	Q14202	447
ZNF292	NCKAP1	Q9Y2A7	447
ZNF292	ZNF385B	Q569K4	444
ZNF292	CDKL5	O76039	433
ZNF292	KLHL7	Q8IXQ5	428

IntAct

29 interactions, top by confidence:

A	B	Type	Score
P4HB	P4HA2	psi-mi:“MI:0914”(association)	0.740
CBX1	ZNF292	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
DCLK3	ZNF292	psi-mi:“MI:0915”(physical association)	0.370
ALB	SH3BP5	psi-mi:“MI:0914”(association)	0.350
APBB1	SSPOP	psi-mi:“MI:0914”(association)	0.350
DYRK1A	TEX13D	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
ATG16L1	ESYT2	psi-mi:“MI:0914”(association)	0.350
GYPA	HYKK	psi-mi:“MI:0914”(association)	0.350
SLAMF1	ZNF292	psi-mi:“MI:0914”(association)	0.350
	PHF20L1	psi-mi:“MI:0914”(association)	0.350
USP20	MYO9A	psi-mi:“MI:0914”(association)	0.350
CBX3	MYL12B	psi-mi:“MI:0914”(association)	0.350
CBX5	ZNF292	psi-mi:“MI:0914”(association)	0.350
SUV39H1	ZNF292	psi-mi:“MI:0914”(association)	0.350
KLF15	ZNF292	psi-mi:“MI:2364”(proximity)	0.270
SOX7	NFIB	psi-mi:“MI:2364”(proximity)	0.270
SRF	ZNF292	psi-mi:“MI:2364”(proximity)	0.270
ZMYM3	TAF4	psi-mi:“MI:2364”(proximity)	0.270
ZNF292	pyrG	psi-mi:“MI:0915”(physical association)	0.000
	ZNF292	psi-mi:“MI:0915”(physical association)	0.000
ZNF292	fadL	psi-mi:“MI:0915”(physical association)	0.000
TIAM1	ZNF292	psi-mi:“MI:0915”(physical association)	0.000
RCAN1	ZNF292	psi-mi:“MI:0915”(physical association)	0.000
HUNK	ZNF292	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (82): ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Affinity Capture-MS), ZNF292 (Proximity Label-MS), ZNF292 (Proximity Label-MS), ZNF292 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0FKI7, A1A5R8, A2AHC3, A2BE28, A5WUN7, A8DZJ1, B7ZS37, D3Z6S9, D3Z8E6, O55036, O60281, O75113, P54274, P62932, P70278, Q08AD1, Q13129, Q16533, Q2T9I9, Q3UMB5, Q5BLK4, Q5H9M0, Q5T4T6, Q5T5Y3, Q5VYS8, Q640U0, Q641E3, Q6DRL4, Q6IRN6, Q6PUR7, Q7Z2Z1, Q7Z7J5, Q86WZ0, Q8BQ33, Q8IZM8, Q8K0S9, Q8NEM2, Q8TEV9

Diamond homologs: O60281, O60315, Q13129, Q8IZM8, Q9DAU9, Q9R0G7, Q9Z2U2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ZNF292	“up-regulates quantity by expression”	GH1	“transcriptional regulation”

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	36
Likely pathogenic	59
Uncertain significance	478
Likely benign	209
Benign	24

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1064834	NM_015021.3(ZNF292):c.4839_4840del (p.Asn1614fs)	Pathogenic
1320796	NM_015021.3(ZNF292):c.6280C>T (p.Arg2094Ter)	Pathogenic
1361326	NM_015021.3(ZNF292):c.6224_6227del (p.Thr2075fs)	Pathogenic
1676031	NM_015021.3(ZNF292):c.5759_5769del (p.Phe1920fs)	Pathogenic
1677664	NM_015021.3(ZNF292):c.3611del (p.Leu1204fs)	Pathogenic
1698954	NM_015021.3(ZNF292):c.6266_6269del (p.Lys2089fs)	Pathogenic
1700144	NM_015021.3(ZNF292):c.2291dup (p.Tyr764Ter)	Pathogenic
1711978	NM_015021.3(ZNF292):c.6823C>T (p.Arg2275Ter)	Pathogenic
1803333	NM_015021.3(ZNF292):c.3432_3436del (p.Asn1144fs)	Pathogenic
1805350	NM_015021.3(ZNF292):c.4450C>T (p.Gln1484Ter)	Pathogenic
2305738	NM_015021.3(ZNF292):c.4837C>T (p.Gln1613Ter)	Pathogenic
2478892	NM_015021.3(ZNF292):c.3990del (p.Phe1330fs)	Pathogenic
2603681	NM_015021.3(ZNF292):c.2605dup (p.Arg869fs)	Pathogenic
2627676	NM_015021.3(ZNF292):c.1414G>T (p.Glu472Ter)	Pathogenic
3068522	NM_015021.3(ZNF292):c.5233C>T (p.Gln1745Ter)	Pathogenic
3194984	NM_015021.3(ZNF292):c.5950_5956del (p.Ile1984fs)	Pathogenic
3255095	NM_015021.3(ZNF292):c.1717del (p.Ile573fs)	Pathogenic
3343936	NM_015021.3(ZNF292):c.6517C>T (p.Arg2173Ter)	Pathogenic
3376205	NM_015021.3(ZNF292):c.3915dup (p.Asn1306Ter)	Pathogenic
3377128	NM_015021.3(ZNF292):c.6239_6240del (p.Arg2080fs)	Pathogenic
3378028	NM_015021.3(ZNF292):c.6001C>T (p.Arg2001Ter)	Pathogenic
3660909	NM_015021.3(ZNF292):c.4429_4432del (p.Asn1477fs)	Pathogenic
3704755	NM_015021.3(ZNF292):c.2870_2871insT (p.Thr958fs)	Pathogenic
3706907	NM_015021.3(ZNF292):c.537del (p.Lys179_Val180insTer)	Pathogenic
3781053	NM_015021.3(ZNF292):c.5112_5113del (p.Asn1705fs)	Pathogenic
3820357	NM_015021.3(ZNF292):c.4810del (p.Ser1604fs)	Pathogenic
3897571	NM_015021.3(ZNF292):c.4789C>T (p.Gln1597Ter)	Pathogenic
4086075	NM_015021.3(ZNF292):c.4098G>A (p.Trp1366Ter)	Pathogenic
431106	NM_015021.3(ZNF292):c.3066_3069del (p.Glu1022fs)	Pathogenic
4687979	NM_015021.3(ZNF292):c.2966_2967del (p.Arg989fs)	Pathogenic

SpliceAI

2449 predictions. Top by Δscore:

Variant	Effect	Δscore
6:87155755:GCCAG:G	donor_gain	1.0000
6:87155757:CAG:C	donor_loss	1.0000
6:87155760:G:GA	donor_loss	1.0000
6:87155760:G:GG	donor_gain	1.0000
6:87155761:T:A	donor_loss	1.0000
6:87233321:AAAGT:A	acceptor_gain	1.0000
6:87233323:A:AG	acceptor_gain	1.0000
6:87233324:G:GG	acceptor_gain	1.0000
6:87233324:GT:G	acceptor_gain	1.0000
6:87243473:A:AG	acceptor_gain	1.0000
6:87243474:G:GT	acceptor_gain	1.0000
6:87243474:GA:G	acceptor_gain	1.0000
6:87243593:GAGA:G	donor_gain	1.0000
6:87243607:GCTTG:G	donor_gain	1.0000
6:87243608:CTTGG:C	donor_loss	1.0000
6:87243610:TGGTG:T	donor_loss	1.0000
6:87243611:GGTG:G	donor_loss	1.0000
6:87243612:G:GG	donor_gain	1.0000
6:87243612:GT:G	donor_loss	1.0000
6:87243613:T:G	donor_loss	1.0000
6:87245500:AAG:A	acceptor_gain	1.0000
6:87245501:A:G	acceptor_gain	1.0000
6:87245502:G:A	acceptor_gain	1.0000
6:87245642:GAG:G	donor_gain	1.0000
6:87254646:ACAG:A	acceptor_loss	1.0000
6:87254647:CAGA:C	acceptor_loss	1.0000
6:87254648:A:AG	acceptor_gain	1.0000
6:87254648:A:AT	acceptor_loss	1.0000
6:87254649:G:GG	acceptor_gain	1.0000
6:87254649:GACT:G	acceptor_gain	1.0000

AlphaMissense

18076 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:87243559:T:C	C276R	1.000
6:87243561:T:G	C276W	1.000
6:87243584:T:C	L284P	1.000
6:87243610:T:A	W293R	1.000
6:87243610:T:C	W293R	1.000
6:87245503:G:C	W293C	1.000
6:87245503:G:T	W293C	1.000
6:87245508:T:C	L295P	1.000
6:87245514:T:C	L297P	1.000
6:87245519:T:A	W299R	1.000
6:87245519:T:C	W299R	1.000
6:87245522:A:C	S300R	1.000
6:87245524:T:A	S300R	1.000
6:87245524:T:G	S300R	1.000
6:87254684:T:C	L352P	1.000
6:87254686:T:C	C353R	1.000
6:87254688:T:G	C353W	1.000
6:87254789:G:C	R387P	1.000
6:87254794:T:C	C389R	1.000
6:87254801:T:A	L391Q	1.000
6:87254801:T:C	L391P	1.000
6:87254809:T:C	F394L	1.000
6:87254810:T:C	F394S	1.000
6:87254811:T:A	F394L	1.000
6:87254811:T:G	F394L	1.000
6:87254813:T:C	L395P	1.000
6:87254836:T:G	Y403D	1.000
6:87254900:T:A	I424K	1.000
6:87254914:C:A	R429S	1.000
6:87254915:G:C	R429P	1.000

dbSNP variants (sampled 300 via entrez): RS1000003309 (6:87165883 G>A,C), RS1000016124 (6:87163363 A>G), RS1000046648 (6:87204849 C>G,T), RS1000048723 (6:87219177 G>A), RS1000049550 (6:87170844 C>G), RS1000060294 (6:87175352 C>G), RS1000096506 (6:87216507 C>A,T), RS1000114759 (6:87240121 T>C), RS1000151281 (6:87222308 TTCTTACATCCATA>T), RS1000176696 (6:87228214 C>T), RS1000182394 (6:87153847 G>C), RS1000206057 (6:87185262 A>T), RS1000206435 (6:87228558 T>C), RS1000247428 (6:87192245 T>G), RS1000274952 (6:87181857 T>A)

Disease associations

OMIM: gene MIM:616213 | disease phenotypes: MIM:619188, MIM:209850, MIM:208000

GenCC curated gene-disease

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Definitive	Autosomal dominant
intellectual developmental disorder, autosomal dominant 64	Strong	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
complex neurodevelopmental disorder	Definitive	AD

Mondo (8): neurodevelopmental disorder (MONDO:0700092), intellectual developmental disorder, autosomal dominant 64 (MONDO:0030934), intellectual disability (MONDO:0001071), complex neurodevelopmental disorder (MONDO:0100038), autism (MONDO:0005260), arterial calcification, generalized, of infancy, 1 (MONDO:0008817), autosomal dominant non-syndromic intellectual disability (MONDO:0015802), microcephaly (MONDO:0001149)

Orphanet (4): Non-specific syndromic intellectual disability (Orphanet:528084), Generalized arterial calcification of infancy (Orphanet:51608), Autosomal dominant non-syndromic intellectual disability (Orphanet:178469), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

40 total (30 of 40 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000218	High palate
HP:0000219	Thin upper lip vermilion
HP:0000252	Microcephaly
HP:0000286	Epicanthus
HP:0000307	Pointed chin
HP:0000316	Hypertelorism
HP:0000319	Smooth philtrum
HP:0000322	Short philtrum
HP:0000331	Short chin
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000378	Cupped ear
HP:0000414	Bulbous nose
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000582	Upslanted palpebral fissure
HP:0000639	Nystagmus
HP:0000664	Synophrys
HP:0000729	Autistic behavior
HP:0000750	Delayed speech and language development
HP:0000954	Single transverse palmar crease
HP:0001212	Prominent fingertip pads
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001276	Hypertonia
HP:0001321	Cerebellar hypoplasia
HP:0001357	Plagiocephaly

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST000893_1	Entorhinal cortical volume (Alzheimer’s disease interaction)	3.000000e-08
GCST006061_42	Atrial fibrillation	1.000000e-08
GCST007673_14	3-month functional outcome in ischaemic stroke (modified Rankin score)	8.000000e-07
GCST009254_6	Cerebellum white matter volume	7.000000e-06
GCST90000047_123	Age at first sexual intercourse	7.000000e-09
GCST90002381_155	Eosinophil count	7.000000e-14
GCST90002382_347	Eosinophil percentage of white cells	3.000000e-24
GCST90002407_267	White blood cell count	7.000000e-17

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0005092	entorhinal cortical volume
EFO:0009603	stroke outcome severity measurement
EFO:0008320	white matter volume measurement
EFO:0009749	age at first sexual intercourse measurement
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D008831	Microcephaly	C05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
D065886	Neurodevelopmental Disorders	F03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	6
sodium arsenite	decreases expression, increases expression	3
cobaltous chloride	increases expression, decreases reaction	2
nickel chloride	increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Cadmium Chloride	increases expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	increases expression	1
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	decreases methylation	1
2-methyl-4-isothiazolin-3-one	decreases expression	1
zinc chloride	decreases reaction, increases expression	1
butyraldehyde	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
cupric chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
acyline	increases expression	1
abrine	increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression	1
Ethanol	affects cotreatment, increases expression	1

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_1443	SJNB-13	Cancer cell line	Male
CVCL_HD18	HEK293 eGFP-ZNF292	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT06310681	Not specified	COMPLETED	Pilot Testing of a Co-adapted Group Programme for Parents/Carers of Children With Complex Neurodisability
NCT07303049	Not specified	NOT_YET_RECRUITING	Cognitive Benefit of Intensive Rehabilitation Using Rhythmic Music Training in Children With Complex Neurodevelopmental Disorder
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development