NCDN

Summary

NCDN (neurochondrin, HGNC:17597) is a protein-coding gene on chromosome 1p34.3, encoding Neurochondrin (Q9UBB6). Probably involved in signal transduction in the nervous system, via increasing cell surface localization of GRM5/mGluR5 and positively regulating its signaling.

This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described.

Source: NCBI Gene 23154 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder with infantile epileptic spasms (Strong, GenCC) — +1 more curated relationship
• Clinical variants (ClinVar): 130 total — 3 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 14
• Druggable target: yes — 1 molecules with ChEMBL bioactivity
• MANE Select transcript: NM_014284

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17597
Approved symbol	NCDN
Name	neurochondrin
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	NCDN-1, NCDN-2
Ensembl gene	ENSG00000020129
Ensembl biotype	protein_coding
OMIM	608458
Entrez	23154

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000356090, ENST00000373243, ENST00000373253, ENST00000423723, ENST00000437806, ENST00000459931, ENST00000868045, ENST00000868046

RefSeq mRNA: 3 — MANE Select: NM_014284 NM_001014839, NM_001014841, NM_014284

CCDS: CCDS30672, CCDS392

Canonical transcript exons

ENST00000373243 — 7 exons

Exon	Start	End
ENSE00000765284	35560326	35561294
ENSE00000765286	35562392	35562633
ENSE00000765287	35563202	35563426
ENSE00000861160	35563767	35563909
ENSE00001459851	35557799	35558223
ENSE00001876996	35565227	35566779
ENSE00003511339	35559107	35559247

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 99.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 59.3183 / max 2981.9551, expressed in 1812 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2103	56.8365	1812
2106	1.3317	93
2102	0.6884	379
2107	0.3173	106
2108	0.0528	20
2105	0.0498	30
2104	0.0419	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle frontal gyrus	UBERON:0002702	99.68	gold quality
Brodmann (1909) area 10	UBERON:0013541	99.54	gold quality
nucleus accumbens	UBERON:0001882	99.40	gold quality
caudate nucleus	UBERON:0001873	99.18	gold quality
right frontal lobe	UBERON:0002810	99.13	gold quality
postcentral gyrus	UBERON:0002581	99.06	gold quality
putamen	UBERON:0001874	98.89	gold quality
prefrontal cortex	UBERON:0000451	98.83	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.77	gold quality
parietal lobe	UBERON:0001872	98.56	gold quality
frontal cortex	UBERON:0001870	98.54	gold quality
cerebellar hemisphere	UBERON:0002245	98.51	gold quality
superior frontal gyrus	UBERON:0002661	98.50	gold quality
cerebellar cortex	UBERON:0002129	98.47	gold quality
cingulate cortex	UBERON:0003027	98.46	gold quality
anterior cingulate cortex	UBERON:0009835	98.46	gold quality
frontal pole	UBERON:0002795	98.45	gold quality
paraflocculus	UBERON:0005351	98.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.34	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	98.23	gold quality
neocortex	UBERON:0001950	98.09	gold quality
Ammon’s horn	UBERON:0001954	98.07	gold quality
lateral nuclear group of thalamus	UBERON:0002736	97.88	gold quality
telencephalon	UBERON:0001893	97.73	gold quality
amygdala	UBERON:0001876	97.72	gold quality
cerebral cortex	UBERON:0000956	97.65	gold quality
cerebellum	UBERON:0002037	97.55	gold quality
temporal lobe	UBERON:0001871	97.35	gold quality
entorhinal cortex	UBERON:0002728	97.22	gold quality
forebrain	UBERON:0001890	97.02	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

109 targeting NCDN, 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-6867-5P	100.00	82.21	3464
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-609	99.82	64.26	505
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-4729	99.69	72.18	4233

Literature-anchored findings (GeneRIF, showing 7)

• In mouse, the encoded protein is a negative regulator of Ca/calmodulin-dependent protein kinase II phosphorylation and is essential for the spatial learning process. (PMID:15790563)
• A protein encoded by this locus was found to be differentially expressed in postmortem brains from patients with atypical frontotemporal lobar degeneration. (PMID:22360420)
• In silico screening for palmitoyl substrates reveals a role for DHHC1/3/10 (zDHHC1/3/11)-mediated neurochondrin palmitoylation in its targeting to Rab5-positive endosomes. (PMID:23687301)
• we demonstrate that neurochondrin has strong isoform selectivity towards the RIIa subunit of PKA with nanomolar affinity (PMID:25916936)
• Schizophrenia subjects compared to controls showed a marked increase in CA1 hippocampal Norbin, and Tamalin proteins (47% and 34% respectively), which are endogenous regulators of mGluR5 signalling and trafficking (PMID:26048293)
• Low norbin expression is associated with Epilepsy. (PMID:29070854)
• Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy. (PMID:33711248)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ncdn	ENSDARG00000098544
mus_musculus	Ncdn	ENSMUSG00000028833
rattus_norvegicus	Ncdn	ENSRNOG00000011751
drosophila_melanogaster	Neurochondrin	FBGN0037447

Protein

Protein identifiers

Neurochondrin — Q9UBB6 (reviewed: Q9UBB6)

All UniProt accessions (3): C9J5H8, Q9UBB6, H7C2R2

UniProt curated annotations — full annotation on UniProt →

Function. Probably involved in signal transduction in the nervous system, via increasing cell surface localization of GRM5/mGluR5 and positively regulating its signaling. Required for the spatial learning process. Acts as a negative regulator of Ca(2+)-calmodulin-dependent protein kinase 2 (CaMK2) phosphorylation. May play a role in modulating melanin-concentrating hormone-mediated functions via its interaction with MCHR1 that interferes with G protein-coupled signal transduction. May be involved in bone metabolism. May also be involved in neurite outgrowth.

Subunit / interactions. Interacts with MCHR1. Interacts with SEMA4C. Interacts with DIAPH1 (via FH3 domain). Interacts with GRM5.

Subcellular location. Cytoplasm. Cytosol. Endosome membrane. Cell projection. Dendrite. Postsynapse.

Tissue specificity. Abundantly expressed in whole adult brain and in all individual brain regions examined, including spinal cord. Weakly expressed in ovary, testis, fetal brain and small intestine.

Post-translational modifications. Palmitoylated. Palmitoylation by ZDHHC1, ZDHHC3 and ZDHHC11 regulates the association of NCDN with endosome membranes. May also be palmitoylated by ZDHHC7.

Disease relevance. Neurodevelopmental disorder with infantile epileptic spasms (NEDIES) [MIM:619373] An autosomal dominant neurodevelopmental disorder characterized by onset of severe and frequent epileptic spasms within the first year of life. Affected individuals have global developmental delay with delayed walking and poor or absent speech. More variable features may include poor overall growth, high-arched palate, and delayed myelination on brain imaging. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the neurochondrin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UBB6-1	1, NCDN1, Neurochondrin-1	yes
Q9UBB6-2	2, NCDN2, Neurochondrin-2

RefSeq proteins (3): NP_001014839, NP_001014841, NP_055099* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008709	Neurochondrin	Family
IPR016024	ARM-type_fold	Homologous_superfamily

Pfam: PF05536

UniProt features (17 total): sequence variant 6, modified residue 5, initiator methionine 2, lipid moiety-binding region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UBB6-F1	88.12	0.69

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 (7): 2, 2, 2, 75, 448, 3, 4

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 310 (showing top): RNGTGGGC_UNKNOWN, AP1_01, PAX4_01, CCAWYNNGAAR_UNKNOWN, GOBP_REGULATION_OF_NEURONAL_SYNAPTIC_PLASTICITY, LFA1_Q6, MAZ_Q6, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, GOBP_VESICLE_MEDIATED_TRANSPORT, CAGGTCC_MIR492, GGGTGGRR_PAX4_03, GGAMTNNNNNTCCY_UNKNOWN, AAAYRNCTG_UNKNOWN

GO Biological Process (4): neuron projection development (GO:0031175), bone resorption (GO:0045453), regulation of neuronal synaptic plasticity (GO:0048168), regulation of postsynaptic neurotransmitter receptor internalization (GO:0099149)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (13): cytosol (GO:0005829), endosome membrane (GO:0010008), membrane (GO:0016020), dendrite (GO:0030425), neuronal cell body (GO:0043025), perikaryon (GO:0043204), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978), cytoplasm (GO:0005737), endosome (GO:0005768), cell projection (GO:0042995), neuron projection (GO:0043005), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
synapse	2
neuron development	1
plasma membrane bounded cell projection organization	1
tissue homeostasis	1
bone remodeling	1
regulation of synaptic plasticity	1
regulation of receptor internalization	1
regulation of biological quality	1
postsynaptic neurotransmitter receptor internalization	1
binding	1
cytoplasm	1
endosome	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
neuron projection	1
dendritic tree	1
somatodendritic compartment	1
cell body	1
neuronal cell body	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1
plasma membrane bounded cell projection	1
cell junction	1

Protein interactions and networks

STRING

1128 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NCDN	GRIK1	P39086	825
NCDN	TAMALIN	Q7Z6J2	774
NCDN	GRIA4	P48058	743
NCDN	GRM5	P41594	733
NCDN	ZNHIT2	Q9UHR6	650
NCDN	GRIK2	Q13002	639
NCDN	AAR2	Q9Y312	611
NCDN	HOMER3	Q9NSC5	595
NCDN	AP3B2	Q13367	574
NCDN	GATM	P50440	549
NCDN	GAP43	P17677	530
NCDN	DNER	Q8NFT8	522
NCDN	IGLON5	A6NGN9	516
NCDN	SLC7A6OS	Q96CW6	496
NCDN	ZIC4	Q8N9L1	487

IntAct

99 interactions, top by confidence:

A	B	Type	Score
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
NCDN	EFHC2	psi-mi:“MI:0915”(physical association)	0.720
EFHC2	NCDN	psi-mi:“MI:0915”(physical association)	0.720
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
RUVBL1	POLR3A	psi-mi:“MI:0914”(association)	0.640
RUVBL2	POLR3A	psi-mi:“MI:0914”(association)	0.640
GYPA	TCAF2	psi-mi:“MI:0914”(association)	0.640
EFTUD2	SART1	psi-mi:“MI:0914”(association)	0.610
TLE5	NCDN	psi-mi:“MI:0915”(physical association)	0.560
KRT75	NCDN	psi-mi:“MI:0915”(physical association)	0.560
PAX6	NCDN	psi-mi:“MI:0915”(physical association)	0.560
ZNF398	NCDN	psi-mi:“MI:0915”(physical association)	0.560
ZBED1	NCDN	psi-mi:“MI:0915”(physical association)	0.560
KIAA1143	AQR	psi-mi:“MI:0914”(association)	0.530
ECD	SNRNP200	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
PTGES3	AIP	psi-mi:“MI:0914”(association)	0.530
CD40	EXOC5	psi-mi:“MI:0914”(association)	0.530
EFTUD2	AQR	psi-mi:“MI:0914”(association)	0.530
SNRNP40	AQR	psi-mi:“MI:0914”(association)	0.530
EAPP	SNRNP200	psi-mi:“MI:0914”(association)	0.530
AAR2	SNRNP200	psi-mi:“MI:0914”(association)	0.530
ILVBL	SLC33A1	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
TINF2	NCDN	psi-mi:“MI:0915”(physical association)	0.510
Prpf8		psi-mi:“MI:0915”(physical association)	0.400

BioGRID (135): NCDN (Two-hybrid), EFHC2 (Two-hybrid), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), NCDN (Affinity Capture-MS), AGPS (Affinity Capture-MS), ALDH3A2 (Affinity Capture-MS), ASAH1 (Affinity Capture-MS), ATP1A1 (Affinity Capture-MS)

ESM2 similar proteins: A0JP94, A1A5F2, A1EC95, A2BID5, A9JRI0, E7FAW3, E7FBU4, E9PVA8, F4HRS2, F4IP13, K8ERU3, O35095, O43299, P42695, P49815, P49816, Q08CY4, Q0DJS1, Q28205, Q2KJ97, Q3U829, Q3UHQ6, Q5JWR5, Q5PRF0, Q5R5R2, Q5SPP5, Q5ZIG0, Q61037, Q640K1, Q642P2, Q68F70, Q6AI08, Q6GN08, Q6GPP1, Q6P1G0, Q6ZNJ1, Q6ZQA0, Q6ZQK0, Q7T006, Q7ZY56

Diamond homologs: O35095, Q2KJ97, Q5ZIG0, Q640K1, Q9UBB6, Q9Z0E0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 110 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Telomere Extension By Telomerase	5	35.1×	1e-04
mRNA Splicing - Minor Pathway	5	17.2×	2e-03
mRNA Splicing - Major Pathway	9	7.6×	7e-04

GO biological processes:

GO term	Partners	Fold	FDR
spliceosomal snRNP assembly	5	29.9×	3e-04
mRNA splicing, via spliceosome	8	7.5×	3e-03
RNA splicing	8	7.3×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	3
Likely pathogenic	4
Uncertain significance	91
Likely benign	19
Benign	1

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
984913	NM_014284.3(NCDN):c.1433G>A (p.Arg478Gln)	Pathogenic
984914	NM_014284.3(NCDN):c.1492T>C (p.Trp498Arg)	Pathogenic
984915	NM_014284.3(NCDN):c.1955C>T (p.Pro652Leu)	Pathogenic
1320191	NM_014284.3(NCDN):c.990dup (p.Glu331fs)	Likely pathogenic
1684580	NM_014284.3(NCDN):c.216dup (p.Arg73fs)	Likely pathogenic
3363194	NM_014284.3(NCDN):c.1598C>T (p.Pro533Leu)	Likely pathogenic
984912	NM_014284.3(NCDN):c.1297G>C (p.Glu433Gln)	Likely pathogenic

SpliceAI

1286 predictions. Top by Δscore:

Variant	Effect	Δscore
1:35559243:TGCTA:T	donor_gain	1.0000
1:35559244:GCTA:G	donor_gain	1.0000
1:35559244:GCTAG:G	donor_gain	1.0000
1:35559246:TA:T	donor_gain	1.0000
1:35559247:AG:A	donor_loss	1.0000
1:35559248:G:GG	donor_gain	1.0000
1:35559249:T:G	donor_loss	1.0000
1:35559253:G:GT	donor_gain	1.0000
1:35559254:A:T	donor_gain	1.0000
1:35561259:G:GT	donor_gain	1.0000
1:35561293:AGG:A	donor_loss	1.0000
1:35561294:GGTGA:G	donor_loss	1.0000
1:35561295:GTGAG:G	donor_loss	1.0000
1:35563427:G:GG	donor_gain	1.0000
1:35563761:TTCCA:T	acceptor_loss	1.0000
1:35563762:TCCAG:T	acceptor_loss	1.0000
1:35563763:CCA:C	acceptor_loss	1.0000
1:35563764:CAGG:C	acceptor_loss	1.0000
1:35563765:A:AG	acceptor_gain	1.0000
1:35563765:AG:A	acceptor_gain	1.0000
1:35563765:AGGC:A	acceptor_gain	1.0000
1:35563766:G:GT	acceptor_gain	1.0000
1:35563766:GG:G	acceptor_gain	1.0000
1:35563766:GGC:G	acceptor_gain	1.0000
1:35563766:GGCG:G	acceptor_gain	1.0000
1:35563766:GGCGT:G	acceptor_gain	1.0000
1:35563908:AGGT:A	donor_loss	1.0000
1:35563909:GGTA:G	donor_loss	1.0000
1:35563910:G:GG	donor_gain	1.0000
1:35559105:A:AG	acceptor_gain	0.9900

AlphaMissense

4634 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:35560863:T:C	F238L	0.999
1:35560865:T:A	F238L	0.999
1:35560865:T:G	F238L	0.999
1:35561089:T:C	L313P	0.999
1:35560386:G:C	A79P	0.998
1:35560411:G:C	R87P	0.998
1:35560984:G:C	R278P	0.998
1:35560996:T:C	L282P	0.998
1:35561162:C:G	C337W	0.998
1:35560380:T:C	F77L	0.997
1:35560382:C:A	F77L	0.997
1:35560382:C:G	F77L	0.997
1:35560395:T:C	F82L	0.997
1:35560397:C:A	F82L	0.997
1:35560397:C:G	F82L	0.997
1:35560414:T:C	L88P	0.997
1:35560470:G:C	G107R	0.997
1:35560471:G:A	G107D	0.997
1:35560837:T:C	F229S	0.997
1:35560864:T:G	F238C	0.997
1:35561002:T:C	L284P	0.997
1:35561037:T:A	W296R	0.997
1:35561037:T:C	W296R	0.997
1:35561092:C:A	A314E	0.997
1:35561163:T:G	Y338D	0.997
1:35562438:G:C	R397P	0.997
1:35562452:T:A	W402R	0.997
1:35562452:T:C	W402R	0.997
1:35559240:T:C	L56P	0.996
1:35560390:T:A	V80D	0.996

dbSNP variants (sampled 300 via entrez): RS1000343223 (1:35558064 T>TG), RS1000465360 (1:35559709 A>G), RS1000797640 (1:35567240 C>T), RS1001378491 (1:35557382 G>A,T), RS1001720162 (1:35556485 T>C), RS1002005085 (1:35561583 A>C), RS1002140888 (1:35561363 G>A,C,T), RS1002345511 (1:35566711 G>A,T), RS1002969501 (1:35557793 G>A), RS1003399692 (1:35563589 G>A,T), RS1003681245 (1:35563580 C>A,T), RS1004513195 (1:35559618 G>T), RS1004855772 (1:35557114 G>A), RS1005462454 (1:35555873 C>A), RS1006948288 (1:35564470 T>C)

Disease associations

OMIM: gene MIM:608458 | disease phenotypes: MIM:619373, MIM:136140

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder with infantile epileptic spasms	Strong	Autosomal dominant
autosomal recessive non-syndromic intellectual disability	Supportive	Autosomal recessive

Mondo (3): neurodevelopmental disorder with infantile epileptic spasms (MONDO:0859162), Floating-Harbor syndrome (MONDO:0007621), autosomal recessive non-syndromic intellectual disability (MONDO:0019502)

Orphanet (1): Floating-Harbor syndrome (Orphanet:2044)

HPO phenotypes

14 total (14 of 14 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000218	High palate
HP:0000286	Epicanthus
HP:0000316	Hypertelorism
HP:0000565	Esotropia
HP:0000750	Delayed speech and language development
HP:0001249	Intellectual disability
HP:0002188	Delayed CNS myelination
HP:0003593	Infantile onset
HP:0004322	Short stature
HP:0007359	Focal-onset seizure
HP:0011097	Epileptic spasm
HP:0031936	Delayed ability to walk
HP:0032794	Myoclonic seizure

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537062	Floating-harbor syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5724619 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,538 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,538

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 3 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.04	IC50	9220	nM	MOLIBRESIB

PubChem BioAssay actives

1 with measured affinity, of 8 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178844: Inhibition of NCDN (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	9.2200	uM

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol B	increases expression	1
bisphenol S	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	increases expression	1
Caffeine	decreases phosphorylation	1
Diuron	decreases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	increases expression	1
Ivermectin	decreases expression	1
Lead	affects splicing, affects expression	1
Selenium	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Thiram	decreases expression	1
Valproic Acid	increases methylation	1
Vitamin E	affects cotreatment, increases expression	1
Okadaic Acid	increases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651873	Binding	Binding affinity to human NCDN incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 induced pluripotent stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_YZ87	KICRi002-A-3	Induced pluripotent stem cell	Male

Clinical trials (associated diseases)

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