CAPS2

Summary

CAPS2 (calcyphosine 2, HGNC:16471) is a protein-coding gene on chromosome 12q21.1-q21.2, encoding Calcyphosin-2 (Q9BXY5).

Calcyphosine-2 is a calcium-binding protein with 2 EF-hand motifs (Wang et al., 2002 [PubMed 11846421]).

Source: NCBI Gene 84698 — RefSeq curated summary.

At a glance

• Gene–disease (curated): intellectual disability (Limited, GenCC)
• Clinical variants (ClinVar): 149 total
• GTEx eGene: eQTL in 38 tissues, sQTL in 10 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.46 (unconstrained)
• MANE Select transcript: NM_001355024
• Notable: 149 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16471
Approved symbol	CAPS2
Name	calcyphosine 2
Location	12q21.1-q21.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000180881
Ensembl biotype	protein_coding
OMIM	607724
Entrez	84698

Gene structure

Transcript identifiers

Ensembl transcripts: 30 — 20 protein_coding, 5 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 retained_intron

MANE Select: ENST00000699294

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 5, TSL 2: 1, TSL 3: 2, TSL 4: 5, TSL 5: 1

ENST00000699294, ENST00000328705, ENST00000336815, ENST00000393284, ENST00000409004, ENST00000409445, ENST00000409799, ENST00000436898, ENST00000486196, ENST00000493070, ENST00000547320, ENST00000548035, ENST00000548958, ENST00000551829, ENST00000552497, ENST00000891113, ENST00000891114, ENST00000891115, ENST00000891116, ENST00000891117, ENST00000891118, ENST00000891119, ENST00000891120, ENST00000891121, ENST00000912723, ENST00000968428, ENST00000968429, ENST00000968430, ENST00000968431, ENST00001030098

RefSeq mRNA: 12 — MANE Select: NM_001355024 NM_001286547, NM_001286548, NM_001355023, NM_001355024, NM_001355025, NM_001355026, NM_001355027, NM_001355030, NM_001355031, NM_001355032, NM_001355033, NM_032606

CCDS: CCDS91727

Canonical transcript exons

ENST00000699294 — 17 exons

Exon	Start	End
ENSE00001356677	75275979	75279065
ENSE00003463742	75323177	75323222
ENSE00003466214	75312848	75312915
ENSE00003488182	75316312	75316434
ENSE00003504878	75284961	75285080
ENSE00003529352	75304757	75304876
ENSE00003536626	75282251	75282347
ENSE00003559516	75321400	75321576
ENSE00003585308	75325239	75325288
ENSE00003611228	75289621	75289775
ENSE00003624673	75298687	75298780
ENSE00003635413	75298871	75298966
ENSE00003637043	75299837	75299911
ENSE00003639214	75291744	75291820
ENSE00003650414	75326418	75326527
ENSE00003663001	75293249	75293367
ENSE00003976185	75329867	75330324

Expression profiles

Bgee: expression breadth ubiquitous, 215 present calls, max score 96.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.6125 / max 108.5483, expressed in 962 samples.

Highest expression (Bgee): bronchial epithelial cell, uterine tube, bronchus, mucosa of paranasal sinus, calcaneal tendon.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CAPS2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 38 tissues and its splicing (sQTL) in 10 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 48 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	9.6e-70	+1.29	12:75298975:A:T
Nerve Tibial	eqtl	5.6e-35	+0.33	12:75338832:ATAAG:A
Artery Tibial	eqtl	7.9e-33	+0.32	12:75316224:C:T
Adipose Subcutaneous	eqtl	2.4e-32	+0.31	12:75327567:T:C
Artery Aorta	eqtl	6.7e-27	+0.34	12:75361240:C:T
Cells Cultured fibroblasts	eqtl	8.7e-22	+0.29	12:75465887:C:T
Colon Transverse	eqtl	5.1e-21	+0.32	12:75393352:G:A
Breast Mammary Tissue	eqtl	1.3e-20	+0.32	12:75331856:C:T
Esophagus Muscularis	eqtl	5.0e-20	+0.30	12:75393352:G:A
Spleen	eqtl	6.1e-19	+0.50	12:75379684:G:A
Adipose Visceral Omentum	eqtl	7.1e-18	+0.25	12:75343517:T:C
Muscle Skeletal	eqtl	1.0e-16	+0.25	12:75343517:T:C
Esophagus Gastroesophageal Junction	eqtl	4.2e-16	+0.35	12:75393352:G:A
Esophagus Mucosa	eqtl	1.2e-15	+0.33	12:75301662:T:C
Thyroid	sqtl	6.5e-14	-0.60	12:75298975:A:T
Pituitary	eqtl	1.2e-13	+0.34	12:75358100:C:T
Colon Sigmoid	eqtl	1.5e-13	+0.32	12:75340104:G:A
Stomach	eqtl	1.3e-11	+0.28	12:75394711:C:G
Nerve Tibial	sqtl	2.1e-11	-0.56	12:75299971:G:A
Thyroid	eqtl	2.2e-10	+0.19	12:75375089:G:T

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
132160	2.1753	877
132159	0.4148	180
132158	0.0224	9

Top tissues by expression

showing 100 of 248 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	96.72	gold quality
right uterine tube	UBERON:0001302	95.57	gold quality
bronchus	UBERON:0002185	95.35	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.38	gold quality
calcaneal tendon	UBERON:0003701	91.03	gold quality
caput epididymis	UBERON:0004358	88.77	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.73	gold quality
corpus callosum	UBERON:0002336	86.14	gold quality
cerebellar hemisphere	UBERON:0002245	84.95	gold quality
cerebellar cortex	UBERON:0002129	84.85	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.74	gold quality
apex of heart	UBERON:0002098	84.03	gold quality
cerebellum	UBERON:0002037	83.99	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.69	gold quality
adrenal tissue	UBERON:0018303	83.39	gold quality
adenohypophysis	UBERON:0002196	83.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.22	gold quality
right frontal lobe	UBERON:0002810	83.05	gold quality
pituitary gland	UBERON:0000007	82.74	gold quality
right atrium auricular region	UBERON:0006631	82.70	gold quality
hindlimb stylopod muscle	UBERON:0004252	82.54	gold quality
hypothalamus	UBERON:0001898	82.25	gold quality
mucosa of stomach	UBERON:0001199	81.99	gold quality
gastrocnemius	UBERON:0001388	81.80	gold quality
muscle of leg	UBERON:0001383	81.76	gold quality
descending thoracic aorta	UBERON:0002345	81.69	gold quality
left ovary	UBERON:0002119	81.54	gold quality
right adrenal gland cortex	UBERON:0035827	81.45	gold quality
anterior cingulate cortex	UBERON:0009835	81.20	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.10	gold quality
cardiac atrium	UBERON:0002081	81.04	gold quality
right adrenal gland	UBERON:0001233	80.87	gold quality
left adrenal gland	UBERON:0001234	80.67	gold quality
left adrenal gland cortex	UBERON:0035825	80.54	gold quality
right ovary	UBERON:0002118	80.44	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	80.38	gold quality
fallopian tube	UBERON:0003889	79.99	gold quality
heart left ventricle	UBERON:0002084	79.83	gold quality
primary visual cortex	UBERON:0002436	79.82	gold quality
adrenal cortex	UBERON:0001235	79.77	gold quality
thoracic aorta	UBERON:0001515	79.66	gold quality
right coronary artery	UBERON:0001625	79.64	gold quality
ascending aorta	UBERON:0001496	79.56	gold quality
adrenal gland	UBERON:0002369	79.52	gold quality
caudate nucleus	UBERON:0001873	79.49	gold quality
islet of Langerhans	UBERON:0000006	79.47	gold quality
aorta	UBERON:0000947	79.34	gold quality
spinal cord	UBERON:0002240	79.31	gold quality
tibial artery	UBERON:0007610	79.27	gold quality
popliteal artery	UBERON:0002250	79.26	gold quality
amygdala	UBERON:0001876	79.19	gold quality
prefrontal cortex	UBERON:0000451	79.13	gold quality
left lobe of thyroid gland	UBERON:0001120	79.01	gold quality
tibial nerve	UBERON:0001323	78.97	gold quality
right lung	UBERON:0002167	78.97	gold quality
cardiac ventricle	UBERON:0002082	78.81	gold quality
heart	UBERON:0000948	78.73	gold quality
left uterine tube	UBERON:0001303	78.51	gold quality
thyroid gland	UBERON:0002046	78.51	gold quality
lower esophagus muscularis layer	UBERON:0035833	78.43	gold quality
lower esophagus	UBERON:0013473	78.42	gold quality
neocortex	UBERON:0001950	78.41	gold quality
brain	UBERON:0000955	78.40	gold quality
frontal cortex	UBERON:0001870	78.37	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	78.34	gold quality
right lobe of thyroid gland	UBERON:0001119	78.09	gold quality
forebrain	UBERON:0001890	78.00	gold quality
body of uterus	UBERON:0009853	77.95	gold quality
left coronary artery	UBERON:0001626	77.83	gold quality
tendon	UBERON:0000043	77.80	gold quality
occipital lobe	UBERON:0002021	77.72	gold quality
gall bladder	UBERON:0002110	77.69	gold quality
substantia nigra	UBERON:0002038	77.59	gold quality
cerebral cortex	UBERON:0000956	77.53	gold quality
metanephros cortex	UBERON:0010533	77.44	gold quality
sural nerve	UBERON:0015488	77.40	gold quality
putamen	UBERON:0001874	77.31	gold quality
endocervix	UBERON:0000458	77.18	gold quality
nucleus accumbens	UBERON:0001882	77.18	gold quality
coronary artery	UBERON:0001621	77.17	gold quality
stromal cell of endometrium	CL:0002255	77.03	gold quality
Brodmann (1909) area 23	UBERON:0013554	76.94	gold quality
cortex of kidney	UBERON:0001225	76.93	gold quality
left testis	UBERON:0004533	76.70	gold quality
right testis	UBERON:0004534	76.64	gold quality
midbrain	UBERON:0001891	76.52	gold quality
Ammon’s horn	UBERON:0001954	76.36	gold quality
ovary	UBERON:0000992	76.26	gold quality
muscle layer of sigmoid colon	UBERON:0035805	75.82	gold quality
uterine cervix	UBERON:0000002	75.62	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.51	gold quality
superior vestibular nucleus	UBERON:0007227	75.30	gold quality
smooth muscle tissue	UBERON:0001135	75.18	gold quality
testis	UBERON:0000473	75.16	gold quality
esophagus	UBERON:0001043	74.77	gold quality
minor salivary gland	UBERON:0001830	74.52	gold quality
ectocervix	UBERON:0012249	74.52	gold quality
peritoneum	UBERON:0002358	74.42	gold quality
omental fat pad	UBERON:0010414	74.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.68

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 156 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Cerebellum	tissue	215.4
Cerebral cortex	tissue	78.6
Somatosensory cortex	tissue	78.6
Occipital cortex	tissue	71.1
Postcentral gyrus	tissue	65.3
Frontal cortex	tissue	45.8
Salivary gland	tissue	45.5
Hippocampal formation	tissue	39.5
Entorhinal cortex	tissue	39.5
Temporal cortex	tissue	37.8
Retrosplenial and cingulate cortex	tissue	36.1
Kidney	tissue	35.8
Amygdala	tissue	30.5
Epididymis	tissue	28.6
Substantia nigra	tissue	28.5
Periaqueductal gray	tissue	28.3
Cervix	tissue	28.0
Motor cortex	tissue	27.1
Pancreas	tissue	24.5
Retrosplenial cortex	tissue	24.3
Insular cortex	tissue	24.0
Choroid plexus	tissue	24.0
Prefrontal cortex	tissue	23.1
Hippocampus	tissue	20.6
Smooth muscle	tissue	20.3
Adrenal gland	tissue	19.9
Midbrain	tissue	19.8
Pons	tissue	19.7
Spinal cord	tissue	19.1
Stomach 1	tissue	18.9
Amygdala	tissue	18.7
Hypothalamus	tissue	18.4
Hippocampal formation	tissue	18.4
Medulla oblongata	tissue	18.3
Choroid plexus	tissue	18.2
Prostate	tissue	18.2
Hypothalamus	tissue	18.0
Thalamus	tissue	17.8
Septum	tissue	17.6
Seminal vesicle	tissue	17.4
Breast	tissue	17.1
Thyroid gland	tissue	17.1
Lung	tissue	17.0
Basal ganglia	tissue	16.5	medium
Substantia nigra	tissue	16.4
Cerebral cortex	tissue	16.1	high
Insular cortex	tissue	16.1
Prefrontal cortex	tissue	15.9
Entorhinal cortex	tissue	15.8
Retrosplenial and cingulate cortex	tissue	15.6
Motor cortex	tissue	15.4
Septum	tissue	15.0
Retrosplenial cortex	tissue	15.0
Temporal cortex	tissue	15.0
Gallbladder	tissue	14.6
Somatosensory cortex	tissue	14.4
Superior colliculi	tissue	14.3
Occipital cortex	tissue	14.2
Endometrium 1	tissue	14.1
Corpus callosum	tissue	13.5

Brain sub-regions (HPA Brain Atlas): detected in 381; highest nTPM — Cerebellar cortex (206.2), Vermis (190.9), Flocculonodular lobe (181.6), Median raphe nucleus (75.6), Postcentral gyrus, middle (61.4).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CAPS2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

11 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-942-5P	99.41	68.40	1977
HSA-MIR-4777-3P	99.15	68.92	626
HSA-MIR-138-2-3P	98.91	68.33	1643
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-4724-3P	97.57	67.31	785
HSA-MIR-383-5P	96.86	67.55	820
HSA-MIR-518E-3P	82.28	65.75	57

Functional genomics

gnomAD constraint: pLI 1.68e-11, LOEUF 1.46, missense Z -0.403 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000393284 — one region, missense o/e 1.06.

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	caps2	ENSDARG00000058486
mus_musculus	Caps2	ENSMUSG00000035694
rattus_norvegicus	Caps2	ENSRNOG00000026600
drosophila_melanogaster	TpnC47D	FBGN0010423
drosophila_melanogaster	TpnC73F	FBGN0010424
drosophila_melanogaster	TpnC41C	FBGN0013348

Paralogs (5): CAPS (ENSG00000105519), PHF24 (ENSG00000122733), CAPSL (ENSG00000152611), EFCAB6 (ENSG00000186976), SPATA21 (ENSG00000187144)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Macaca fascicularis	Q4R8T1	94.7%	Diamond
Pongo abelii	Q5RE62	94.6%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
CAPS2-AS1	ncRNA	107983975
GLIPR1L1	protein-coding	256710
KCNC2	protein-coding	3747
GLIPR1L2	protein-coding	144321
KRR1	protein-coding	11103
GLIPR1-AS1	ncRNA	123706544
GLIPR1	protein-coding	11010

Protein

Protein identifiers

Calcyphosin-2 — Q9BXY5 (reviewed: Q9BXY5)

Alternative names: Calcyphosine-2

All UniProt accessions (7): B9A061, C9J524, F8VWP7, F8VZC3, F8W927, H7BXT1, Q9BXY5

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Abundantly expressed in many tissues. Expressed in brain, colon, heart, kidney, liver, lung, liver, pancreas, placenta, skeletal muscle, testis and thymus. Highest expression in colon, testis, lung, placenta and brain.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9BXY5-1	1	yes
Q9BXY5-2	2
Q9BXY5-3	3
Q9BXY5-4	4
Q9BXY5-5	5

RefSeq proteins (12): NP_001273476, NP_001273477, NP_001341952, NP_001341953, NP_001341954, NP_001341955, NP_001341956, NP_001341959, NP_001341960, NP_001341961, NP_001341962, NP_115995 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR051581	Ca-bind	Family
IPR057461	CAYP2_PH	Domain

Pfam: PF13499, PF25348

UniProt features (25 total): binding site 12, splice variant 4, domain 3, sequence conflict 2, chain 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BXY5-F1	70.30	0.33

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm; vesicles

Antibody reliability (HPA): IF approved

Functional residue map

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

Ligand- & substrate-binding residues (12)

Position	Role
479	Ca(2+)
481	Ca(2+)
486	Ca(2+)
511	Ca(2+)
513	Ca(2+)
515	Ca(2+)
517	Ca(2+)
522	Ca(2+)
439	Ca(2+)
443	Ca(2+)
450	Ca(2+)
477	Ca(2+)

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 161 (showing top): GOBP_DENDRITE_DEVELOPMENT, GOBP_HINDBRAIN_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_BEHAVIOR, GOBP_NEUROGENESIS, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_FOREBRAIN_GENERATION_OF_NEURONS, GOBP_CEREBRAL_CORTEX_NEURON_DIFFERENTIATION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_HIPPOCAMPUS_DEVELOPMENT, chr12q21, GOBP_BIOLOGICAL_PROCESS_INVOLVED_IN_INTRASPECIES_INTERACTION_BETWEEN_ORGANISMS, GOBP_PALLIUM_DEVELOPMENT, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, GOBP_SECRETION

GO Molecular Function (2): calcium ion binding (GO:0005509), metal ion binding (GO:0046872)

GO top-level categories

2 GO namespaces:

Category	Terms
metal ion binding	1
cation binding	1

Protein interactions and networks

STRING

showing 15 of 453 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAPS2	KISS1R	Q969F8	470
CAPS2	KISS1	Q15726	406
CAPS2	GRTP1	Q5TC63	390
CAPS2	FAABTP	Q96HH6	370
CAPS2	ANO9	A1A5B4	369
CAPS2	SERGEF	Q9UGK8	363
CAPS2	SAAL1	Q96ER3	362
CAPS2	PLPPR1	Q8TBJ4	357
CAPS2	GTF2H1	P32780	356
CAPS2	CAPS	Q13938	354
CAPS2	IPO11	Q9UI26	303
CAPS2	PKP3	Q9Y446	297
CAPS2	VAV3	Q9UKW4	294
CAPS2	SWAP70	Q9UH65	292
CAPS2	DEF6	Q9H4E7	292

IntAct

BioGRID (2 interactions; top human partners by supporting records): PARP10 (Proximity Label-MS), PARP2 (Proximity Label-MS)

Disease & clinical

Genetic variants

Variant evidence for CAPS2: 149 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	121
Likely benign	6
Benign	3

AlphaMissense

484 missense substitutions predicted likely pathogenic (of 3,707 scored), across 155 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M514	9	0.815	0.942
F297	8	0.882	0.981
D364	8	0.864	0.921
D235	8	0.827	0.913
D530	8	0.789	0.893
F318	7	0.905	0.968
F526	7	0.862	0.970
R518	7	0.857	0.971
F332	7	0.850	0.969
E328	7	0.820	0.902
D321	7	0.766	0.827
E516	7	0.750	0.855
H350	7	0.726	0.912
F373	6	0.853	0.961
W490	6	0.801	0.936
G333	6	0.796	0.913
G315	5	0.948	0.985
Y360	5	0.924	0.983
F506	5	0.882	0.939
R311	5	0.881	0.945

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	1.05e-06
Pancreatic Adenocarcinoma (validation)	favorable	9.12e-06

Disease associations

OMIM: gene MIM:607724 | disease phenotypes:

GenCC curated gene-disease

1 curated gene-disease records:

Disease	Classification	Inheritance	Records
intellectual disability	Limited	Autosomal recessive

Mondo (1): intellectual disability (MONDO:0001071)

MeSH disease descriptors

1 disease descriptors:

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	5
trichostatin A	affects cotreatment, decreases expression	3
bisphenol A	affects cotreatment, increases expression, increases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
bufotalin	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
jinfukang	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Glyphosate	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	increases abundance, increases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 204 trials:

NCT	Phase	Status	Title
NCT05657860	Phase 4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	Phase 4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	Phase 4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	Phase 4	RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	Phase 3	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
NCT02304302	Phase 2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	Phase 2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	Phase 2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	Phase 2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	Phase 1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	Phase 1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	Phase 1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	Phase 1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	Phase 1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	Phase 2/3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	Phase 1/2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	Early Phase 1	TERMINATED	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders
NCT02862808	Not specified	COMPLETED	Molecular Diagnosis of Syndromic or Isolated Severe Intellectual Disability Using Whole Exome Sequencing : a Pilot Study
NCT02881333	Not specified	UNKNOWN	Various Type of Genetic Events in Patients With Intellectual Disability
NCT02889068	Not specified	COMPLETED	Targeted Next Generation Sequencing and Intellectual Disability
NCT02914951	Not specified	ENROLLING_BY_INVITATION	Cognitive-Behavioral Therapy for Irritability in Children With Autism Spectrum Disorder and Intellectual Disability
NCT02919826	Not specified	COMPLETED	Dialectical Behaviour Group Therapy for Adults With Intellectual Disabilities
NCT02934854	Not specified	WITHDRAWN	Biomarker for Creatine Deficiency Syndromes (BioCDS)
NCT03033797	Not specified	UNKNOWN	Augmentative and Alternative Communication in Games With Virtual Reality in Intellectual Disabilities
NCT03135236	Not specified	COMPLETED	Parents as the Primary Sexuality Educators for Their Young Adults With Down Syndrome
NCT03139760	Not specified	COMPLETED	POWERSforID: A Telehealth Weight Management System for Adults With Intellectual Disability
NCT03203226	Not specified	COMPLETED	The Feldenkrais Method for People With Intellectual Disability
NCT03212092	Not specified	COMPLETED	Reducing Aggression Among People With an Intellectual Disability
NCT03218462	Not specified	COMPLETED	Effect of Sensory Adapted Dental Environment on Dental Anxiety of Children With Intellectual and Developmental Disabilities
NCT03234231	Not specified	UNKNOWN	Supervised Brushing Programme for Intellectual Disabled Students
NCT03348124	Not specified	UNKNOWN	Prevention Among Young People With Intellectual Disability
NCT03424772	Not specified	UNKNOWN	Whole Genome Sequencing in the Detection of Rare Undiagnosed Genetic Diseases in Children in China
NCT03426059	Not specified	COMPLETED	Mapping the Phenotype in Adults With Phelan-McDermid Syndrome
NCT03492060	Not specified	RECRUITING	Longitudinal Study of Neurogenetic Disorders
NCT03501914	Not specified	COMPLETED	A Pilot Trial of Mindfulness Based Intervention Program for People With Intellectual Disabilities in a Low Income Setting
NCT03522337	Not specified	COMPLETED	Oral Health Promotion Among Preschool Children With Special Needs
NCT03525431	Not specified	COMPLETED	Clinical Utility of Pediatric Whole Exome Sequencing