ACAP3

Summary

ACAP3 (ArfGAP with coiled-coil, ankyrin repeat and PH domains 3, HGNC:16754) is a protein-coding gene on chromosome 1p36.33, encoding Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 (Q96P50). GTPase-activating protein for the ADP ribosylation factor family.

Predicted to enable GTPase activator activity and zinc ion binding activity. Predicted to act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in endosome membrane and growth cone.

Source: NCBI Gene 116983 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 272 total — 78 pathogenic, 3 likely-pathogenic
• MANE Select transcript: NM_030649

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16754
Approved symbol	ACAP3
Name	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3
Location	1p36.33
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1716
Ensembl gene	ENSG00000131584
Ensembl biotype	protein_coding
Entrez	116983

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 17 protein_coding, 8 retained_intron, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000353662, ENST00000354700, ENST00000354980, ENST00000379037, ENST00000438966, ENST00000467278, ENST00000470659, ENST00000472541, ENST00000476572, ENST00000478065, ENST00000479108, ENST00000492936, ENST00000493992, ENST00000892719, ENST00000892720, ENST00000969099, ENST00000969100, ENST00000969101, ENST00000969102, ENST00000969103, ENST00000969104, ENST00000969105, ENST00000969106, ENST00000969107, ENST00000969108, ENST00000969109, ENST00000969110, ENST00000969111

RefSeq mRNA: 1 — MANE Select: NM_030649 NM_030649

CCDS: CCDS19

Canonical transcript exons

ENST00000354700 — 24 exons

Exon	Start	End
ENSE00001889322	1292391	1293708
ENSE00001927436	1307769	1307930
ENSE00003487130	1303162	1303281
ENSE00003495947	1294090	1294199
ENSE00003515599	1299831	1299905
ENSE00003517853	1300509	1300692
ENSE00003522844	1302922	1302975
ENSE00003524130	1294718	1294816
ENSE00003542543	1293823	1293933
ENSE00003547404	1298567	1298679
ENSE00003555901	1301988	1302046
ENSE00003556959	1304086	1304143
ENSE00003563439	1296425	1296633
ENSE00003576054	1295736	1295938
ENSE00003582087	1299345	1299356
ENSE00003582645	1295447	1295554
ENSE00003591650	1296015	1296109
ENSE00003615234	1297822	1297933
ENSE00003622960	1300158	1300202
ENSE00003640098	1298370	1298421
ENSE00003655822	1296211	1296280
ENSE00003673334	1299973	1300068
ENSE00003673746	1294402	1294628
ENSE00003689281	1298013	1298113

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 99.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.2250 / max 64.1136, expressed in 1654 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9748	4.0329	1551
9750	0.3796	198
9749	0.3047	171
9747	0.2748	122
201311	0.2330	95

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.74	gold quality
cerebellar hemisphere	UBERON:0002245	99.68	gold quality
cerebellar cortex	UBERON:0002129	99.64	gold quality
cerebellum	UBERON:0002037	99.15	gold quality
right frontal lobe	UBERON:0002810	98.80	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.36	gold quality
adenohypophysis	UBERON:0002196	98.28	gold quality
skin of abdomen	UBERON:0001416	98.08	gold quality
skin of leg	UBERON:0001511	97.99	gold quality
pituitary gland	UBERON:0000007	97.68	gold quality
ectocervix	UBERON:0012249	97.66	gold quality
nucleus accumbens	UBERON:0001882	97.65	gold quality
lower esophagus mucosa	UBERON:0035834	97.62	gold quality
anterior cingulate cortex	UBERON:0009835	97.61	gold quality
left uterine tube	UBERON:0001303	97.52	gold quality
body of uterus	UBERON:0009853	97.49	gold quality
putamen	UBERON:0001874	97.45	gold quality
apex of heart	UBERON:0002098	97.37	gold quality
cortical plate	UBERON:0005343	97.21	gold quality
endocervix	UBERON:0000458	97.15	gold quality
caudate nucleus	UBERON:0001873	97.09	gold quality
right ovary	UBERON:0002118	97.01	gold quality
muscle layer of sigmoid colon	UBERON:0035805	96.97	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.96	gold quality
amygdala	UBERON:0001876	96.95	gold quality
left ovary	UBERON:0002119	96.79	gold quality
lower esophagus	UBERON:0013473	96.61	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.61	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.60	gold quality
ganglionic eminence	UBERON:0004023	96.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting ACAP3, 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-4283	100.00	66.42	2097
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-6837-5P	99.25	65.47	1632

Literature-anchored findings (GeneRIF, showing 3)

• minisatellite locus UPS29 can regulate an activity of CENTB5, SCNN1D and ACOT7 in nervous system cells. (PMID:19548526)
• Length Polymorphism and Methylation Status of UPS29 Minisatellite of the ACAP3 Gene as Molecular Biomarker of Epilepsy. Sex Differences in Seizure Types and Symptoms. (PMID:33276684)
• ACAP3 negatively regulated by HDAC2 inhibits the malignant development of papillary thyroid carcinoma cells. (PMID:39098591)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	acap3a	ENSDARG00000075990
danio_rerio	acap3b	ENSDARG00000099240
		ENSDARG00000115609
mus_musculus	Acap3	ENSMUSG00000029033
rattus_norvegicus	Acap3	ENSRNOG00000022307

Paralogs (28): ARAP2 (ENSG00000047365), ACAP1 (ENSG00000072818), SMAP2 (ENSG00000084070), ASAP3 (ENSG00000088280), ARFGAP1 (ENSG00000101199), ADAP1 (ENSG00000105963), AGFG2 (ENSG00000106351), GIT1 (ENSG00000108262), SMAP1 (ENSG00000112305), ACAP2 (ENSG00000114331), ARAP3 (ENSG00000120318), AGAP3 (ENSG00000133612), AGAP2 (ENSG00000135439), APPL2 (ENSG00000136044), GIT2 (ENSG00000139436), ARFGAP2 (ENSG00000149182), ASAP2 (ENSG00000151693), ASAP1 (ENSG00000153317), APPL1 (ENSG00000157500), AGAP1 (ENSG00000157985), AGAP5 (ENSG00000172650), AGFG1 (ENSG00000173744), ADAP2 (ENSG00000184060), ARAP1 (ENSG00000186635), AGAP4 (ENSG00000188234), AGAP6 (ENSG00000204149), AGAP9 (ENSG00000204172), ARFGAP3 (ENSG00000242247)

Protein

Protein identifiers

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 3 — Q96P50 (reviewed: Q96P50)

Alternative names: Centaurin-beta-5

All UniProt accessions (2): Q96P50, F8W850

UniProt curated annotations — full annotation on UniProt →

Function. GTPase-activating protein for the ADP ribosylation factor family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q96P50-3	1	yes
Q96P50-1	2
Q96P50-4	3

RefSeq proteins (1): NP_085152* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001164	ArfGAP_dom	Domain
IPR001849	PH_domain	Domain
IPR002110	Ankyrin_rpt	Repeat
IPR004148	BAR_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR037278	ARFGAP/RecO	Homologous_superfamily
IPR038508	ArfGAP_dom_sf	Homologous_superfamily
IPR042695	ACAP3_BAR	Domain
IPR045258	ACAP1/2/3-like	Family

Pfam: PF00169, PF01412, PF12796, PF16746

UniProt features (15 total): splice variant 3, repeat 3, domain 2, compositionally biased region 2, region of interest 2, chain 1, sequence conflict 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96P50-F1	76.31	0.52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 115 (showing top): GOBP_NEUROGENESIS, USF_C, NFKB_C, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, TGACATY_UNKNOWN, GOBP_NEURON_MIGRATION, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, RYTTCCTG_ETS2_B, GOCC_NEURON_PROJECTION, KEGG_ENDOCYTOSIS, GOBP_CELL_PROJECTION_ORGANIZATION, MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP, USF2_Q6, GOCC_AXON, MYC_Q2

GO Biological Process (2): neuron migration (GO:0001764), regulation of neuron projection development (GO:0010975)

GO Molecular Function (4): GTPase activator activity (GO:0005096), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): cytoplasm (GO:0005737), growth cone (GO:0030426)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell migration	1
generation of neurons	1
neuron projection development	1
regulation of plasma membrane bounded cell projection organization	1
GTPase activity	1
enzyme activator activity	1
GTPase regulator activity	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
site of polarized growth	1
distal axon	1

Protein interactions and networks

STRING

892 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ACAP3	UBE2J2	Q8N2K1	624
ACAP3	PUSL1	Q8N0Z8	595
ACAP3	SCNN1D	P51172	577
ACAP3	AGFG2	O95081	426
ACAP3	C19orf47	Q8N9M1	367
ACAP3	SCNN1B	P51168	349
ACAP3	PRSS36	Q5K4E3	348
ACAP3	ARF6	P26438	347
ACAP3	ZNF410	Q86VK4	347
ACAP3	NEMF	O60524	327
ACAP3	CDCP2	Q5VXM1	325
ACAP3	PRMT2IP	Q6ZRI6	317
ACAP3	ICA1L	Q8NDH6	313
ACAP3	PLEKHN1	Q494U1	307
ACAP3	TXNL4B	Q9NX01	306
ACAP3	C1QTNF12	Q5T7M4	306

IntAct

12 interactions, top by confidence:

A	B	Type	Score
TXNDC16	FOXRED2	psi-mi:“MI:0914”(association)	0.730
ACAP2	ACAP3	psi-mi:“MI:0915”(physical association)	0.640
ACAP3	ACAP2	psi-mi:“MI:0915”(physical association)	0.640
RBM25	PRPF40A	psi-mi:“MI:0914”(association)	0.560
ACAP3	TAB1	psi-mi:“MI:0915”(physical association)	0.370
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
TXNDC16	SEMG1	psi-mi:“MI:0914”(association)	0.350
ACAP3	SEPTIN6	psi-mi:“MI:0914”(association)	0.350
ITGB3BP	ACAP3	psi-mi:“MI:0915”(physical association)	0.000
SLC35G2	ACAP3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): ACAP3 (Affinity Capture-MS), ACAP3 (Affinity Capture-MS), ACAP3 (Two-hybrid), ACAP3 (Affinity Capture-RNA), SEPT10 (Affinity Capture-MS), SEPT2 (Affinity Capture-MS), ACAP3 (Affinity Capture-MS), ACAP3 (Affinity Capture-MS), ACAP2 (Affinity Capture-MS), SEPT5 (Affinity Capture-MS), SEPT7 (Affinity Capture-MS), SEPT6 (Affinity Capture-MS), FBXW11 (Affinity Capture-MS), HIF1AN (Affinity Capture-MS), SEPT11 (Affinity Capture-MS)

ESM2 similar proteins: A2AAJ9, A2ABU4, A2RUH7, B4GBH0, D3ZGQ5, O09127, O70468, O75038, O88599, O95382, P16419, P21709, P22455, P22607, P29322, P54760, P54761, P55144, P55146, P56741, P70218, P70402, Q00653, Q06418, Q13203, Q13308, Q13425, Q14896, Q15746, Q290N5, Q32P44, Q4LDD4, Q5FW53, Q5PQM4, Q5VST9, Q5VTT5, Q60750, Q61851, Q68LP1, Q80UW5

Diamond homologs: A1L520, A1Z7A6, A5PK26, A6NIR3, O43150, O74345, O75689, O80925, O82171, O94601, O97902, P35197, P38682, P40529, P52594, Q04412, Q09531, Q0WQQ1, Q10165, Q10367, Q14161, Q15027, Q15057, Q17R07, Q1AAU6, Q1ZXH8, Q28CM8, Q2TA45, Q3MID3, Q3UHD9, Q4KLH5, Q4KLN7, Q4LDD4, Q4R4C9, Q5F413, Q5FVC7, Q5R787, Q5RAT7, Q5U464, Q5VTM2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	78
Likely pathogenic	3
Uncertain significance	145
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1341246	GRCh37/hg19 1p36.33-36.32(chr1:849466-2621542)x1	Pathogenic
144707	GRCh38/hg38 1p36.33-36.32(chr1:844347-4398122)x1	Pathogenic
144721	GRCh38/hg38 1p36.33(chr1:1013081-1722599)x1	Pathogenic
145360	GRCh38/hg38 1p36.33-36.31(chr1:844353-5827192)x3	Pathogenic
147521	GRCh38/hg38 1p36.33-36.22(chr1:844347-12470133)x1	Pathogenic
147545	GRCh38/hg38 1p36.33-36.32(chr1:874379-4973261)x1	Pathogenic
148305	GRCh38/hg38 1p36.33-36.32(chr1:1022094-4665295)x1	Pathogenic
148916	GRCh38/hg38 1p36.33-36.32(chr1:821713-5239643)x1	Pathogenic
149171	GRCh38/hg38 1p36.33-36.32(chr1:821713-3569891)x1	Pathogenic
149739	GRCh38/hg38 1p36.33-36.32(chr1:844353-3153909)x1	Pathogenic
150995	GRCh38/hg38 1p36.33-36.32(chr1:821713-3438208)x1	Pathogenic
151451	GRCh38/hg38 1p36.33-36.32(chr1:778698-4898439)x1	Pathogenic
152050	GRCh38/hg38 1p36.33-36.31(chr1:821713-5480263)x1	Pathogenic
152331	GRCh38/hg38 1p36.33-36.32(chr1:914086-2465738)x1	Pathogenic
152333	GRCh38/hg38 1p36.33-36.32(chr1:914086-3305463)x1	Pathogenic
152675	GRCh38/hg38 1p36.33-36.32(chr1:821713-2636393)x1	Pathogenic
152849	GRCh38/hg38 1p36.33-36.32(chr1:821713-4225085)x1	Pathogenic
153078	GRCh38/hg38 1p36.33-36.22(chr1:902111-9556305)x1	Pathogenic
153195	GRCh38/hg38 1p36.33-36.32(chr1:914086-3587042)x1	Pathogenic
153663	GRCh38/hg38 1p36.33-36.22(chr1:914086-9567122)x1	Pathogenic
154548	GRCh38/hg38 1p36.33-36.22(chr1:911300-9329925)x1	Pathogenic
154642	GRCh38/hg38 1p36.33-36.23(chr1:844347-7870545)x1	Pathogenic
155157	GRCh38/hg38 1p36.33(chr1:914086-1613769)x1	Pathogenic
160923	GRCh38/hg38 1p36.33-36.32(chr1:844347-2627474)x1	Pathogenic
1684638	Single allele	Pathogenic
1703627	GRCh37/hg19 1p36.33-36.31(chr1:849466-5625566)	Pathogenic
1703628	GRCh37/hg19 1p36.33-36.32(chr1:849466-4183006)	Pathogenic
1703629	GRCh37/hg19 1p36.33-36.22(chr1:849466-10258804)	Pathogenic
1706500	GRCh37/hg19 1p36.33-36.32(chr1:849466-2518608)x1	Pathogenic
2501007	GRCh37/hg19 1p36.33-36.32(chr1:1-2580976)x1	Pathogenic

SpliceAI

4464 predictions. Top by Δscore:

Variant	Effect	Δscore
1:1293817:GCTCA:G	donor_loss	1.0000
1:1293818:CTCA:C	donor_loss	1.0000
1:1293819:TCACA:T	donor_loss	1.0000
1:1293820:CA:C	donor_loss	1.0000
1:1293821:A:AC	donor_gain	1.0000
1:1293821:ACAG:A	donor_loss	1.0000
1:1293822:C:CT	donor_gain	1.0000
1:1293822:CA:C	donor_gain	1.0000
1:1293822:CAG:C	donor_gain	1.0000
1:1293822:CAGTG:C	donor_gain	1.0000
1:1294625:CCCT:C	acceptor_gain	1.0000
1:1294626:CCTC:C	acceptor_gain	1.0000
1:1294629:C:CC	acceptor_gain	1.0000
1:1294716:AC:A	donor_gain	1.0000
1:1294716:ACCCT:A	donor_gain	1.0000
1:1294717:CC:C	donor_gain	1.0000
1:1294717:CCCTC:C	donor_gain	1.0000
1:1294720:T:TA	donor_gain	1.0000
1:1295443:TTA:T	donor_loss	1.0000
1:1295444:TACT:T	donor_loss	1.0000
1:1295445:A:AC	donor_gain	1.0000
1:1295446:C:CT	donor_gain	1.0000
1:1295446:CT:C	donor_gain	1.0000
1:1295446:CTG:C	donor_gain	1.0000
1:1295446:CTGCG:C	donor_gain	1.0000
1:1295550:GCCCA:G	acceptor_gain	1.0000
1:1295551:CCCA:C	acceptor_gain	1.0000
1:1295551:CCCAC:C	acceptor_gain	1.0000
1:1295552:CCA:C	acceptor_gain	1.0000
1:1295552:CCAC:C	acceptor_gain	1.0000

AlphaMissense

5472 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:1293823:A:G	L787P	1.000
1:1296231:A:G	W463R	1.000
1:1296231:A:T	W463R	1.000
1:1296236:T:A	D461V	1.000
1:1296256:C:A	K454N	1.000
1:1296256:C:G	K454N	1.000
1:1296280:C:A	R446S	1.000
1:1296280:C:G	R446S	1.000
1:1296425:C:A	R446M	1.000
1:1296425:C:G	R446T	1.000
1:1296429:G:C	H445D	1.000
1:1296434:C:T	G443D	1.000
1:1296437:G:A	S442F	1.000
1:1296439:G:C	C441W	1.000
1:1296441:A:G	C441R	1.000
1:1296448:G:C	C438W	1.000
1:1296449:C:T	C438Y	1.000
1:1296450:A:G	C438R	1.000
1:1296472:G:C	S430R	1.000
1:1296472:G:T	S430R	1.000
1:1296474:T:G	S430R	1.000
1:1296478:C:A	W428C	1.000
1:1296478:C:G	W428C	1.000
1:1296480:A:G	W428R	1.000
1:1296480:A:T	W428R	1.000
1:1296510:A:G	C418R	1.000
1:1297888:C:A	W354C	1.000
1:1297888:C:G	W354C	1.000
1:1297890:A:G	W354R	1.000
1:1297890:A:T	W354R	1.000

dbSNP variants (sampled 300 via entrez): RS1000013557 (1:1307957 G>C,T), RS1000022315 (1:1296519 T>G), RS1000056560 (1:1296315 G>A), RS1000090854 (1:1301823 C>G,T), RS1000236370 (1:1300912 C>T), RS1000249074 (1:1305384 G>A,C,T), RS1000287515 (1:1292237 G>A), RS1000313532 (1:1296691 C>G,T), RS1000366586 (1:1292700 G>A), RS1000473668 (1:1309380 G>A,C), RS1000778377 (1:1308812 C>G,T), RS1001132193 (1:1307695 A>C,G), RS1001695904 (1:1298490 A>C,G), RS1001720201 (1:1295457 A>G), RS1002040214 (1:1299168 A>G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:615349, MIM:271640, MIM:607872, MIM:619343

GenCC curated gene-disease

Mondo (5): Ehlers-Danlos syndrome, spondylodysplastic type, 2 (MONDO:0014139), spondyloepimetaphyseal dysplasia with joint laxity (MONDO:0019675), chromosome 1p36 deletion syndrome (MONDO:0011929), chromosome 1p36 deletion syndrome, proximal (MONDO:0859155), neurodevelopmental disorder (MONDO:0700092)

Orphanet (4): B3GALT6-related spondylodysplastic Ehlers-Danlos syndrome (Orphanet:536467), B4GALT7-related spondylodysplastic Ehlers-Danlos syndrome (Orphanet:75496), 1p36 deletion syndrome (Orphanet:1606), OBSOLETE: Spondyloepimetaphyseal dysplasia with joint laxity (Orphanet:93359)

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST004131_103	Inflammatory bowel disease	2.000000e-07
GCST004133_40	Ulcerative colitis	3.000000e-06

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625
C535362	Chromosome 1p36 Deletion Syndrome (supp.)
C562968	Spondyloepimetaphyseal Dysplasia With Joint Laxity (supp.)

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
sodium arsenite	increases expression, affects cotreatment, decreases expression, increases abundance	2
Acetaminophen	increases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
beta-lapachone	decreases expression	1
manganese chloride	decreases expression, increases abundance, affects cotreatment	1
abrine	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Aspirin	increases expression	1
Catechin	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Toluene	decreases expression, increases methylation	1
Valproic Acid	increases methylation	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Acrylamide	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

204 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,
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
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
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
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02381457	Not specified	COMPLETED	SNP-based Microdeletion and Aneuploidy RegisTry (SMART)
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
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism