BLOC1S1

Summary

BLOC1S1 (biogenesis of lysosomal organelles complex 1 subunit 1, HGNC:4200) is a protein-coding gene on chromosome 12q13.2, encoding Biogenesis of lysosome-related organelles complex 1 subunit 1 (P78537). Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes.

BLOC1S1 is a component of the ubiquitously expressed BLOC1 multisubunit protein complex. BLOC1 is required for normal biogenesis of specialized organelles of the endosomal-lysosomal system, such as melanosomes and platelet dense granules (Starcevic and Dell’Angelica, 2004 [PubMed 15102850]).

Source: NCBI Gene 2647 — RefSeq curated summary.

At a glance

• Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC) — +1 more curated relationship
• GWAS associations: 1
• Clinical variants (ClinVar): 31 total
• MANE Select transcript: NM_001487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:4200
Approved symbol	BLOC1S1
Name	biogenesis of lysosomal organelles complex 1 subunit 1
Location	12q13.2
Locus type	gene with protein product
Status	Approved
Aliases	BLOS1, BORCS1
Ensembl gene	ENSG00000135441
Ensembl biotype	protein_coding
OMIM	601444
Entrez	2647

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 nonsense_mediated_decay

ENST00000547076, ENST00000548556, ENST00000548925, ENST00000549147, ENST00000551926, ENST00000553100, ENST00000915709, ENST00000915710

RefSeq mRNA: 1 — MANE Select: NM_001487 NM_001487

CCDS: CCDS8889

Canonical transcript exons

ENST00000548925 — 4 exons

Exon	Start	End
ENSE00000920089	55719499	55719703
ENSE00002427007	55716046	55716196
ENSE00003580603	55716933	55717005
ENSE00003678910	55719091	55719223

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.02.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 76.2480 / max 849.9626, expressed in 1825 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
125968	60.3384	1825
125969	9.8688	1775
125972	2.0396	1053
125971	1.9445	1173
125970	1.2849	968
125973	0.7288	422
206738	0.0430	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	99.02	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.80	gold quality
substantia nigra	UBERON:0002038	98.76	gold quality
amygdala	UBERON:0001876	98.71	gold quality
temporal lobe	UBERON:0001871	98.70	gold quality
lower esophagus mucosa	UBERON:0035834	98.67	gold quality
putamen	UBERON:0001874	98.63	gold quality
Ammon’s horn	UBERON:0001954	98.62	gold quality
granulocyte	CL:0000094	98.61	gold quality
hindlimb stylopod muscle	UBERON:0004252	98.59	gold quality
transverse colon	UBERON:0001157	98.52	gold quality
prefrontal cortex	UBERON:0000451	98.49	gold quality
caudate nucleus	UBERON:0001873	98.48	gold quality
primary visual cortex	UBERON:0002436	98.46	gold quality
rectum	UBERON:0001052	98.44	gold quality
body of stomach	UBERON:0001161	98.41	gold quality
right adrenal gland	UBERON:0001233	98.41	gold quality
anterior cingulate cortex	UBERON:0009835	98.39	gold quality
fundus of stomach	UBERON:0001160	98.37	gold quality
nucleus accumbens	UBERON:0001882	98.37	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.37	gold quality
adult mammalian kidney	UBERON:0000082	98.35	gold quality
hypothalamus	UBERON:0001898	98.35	gold quality
colon	UBERON:0001155	98.32	gold quality
gastrocnemius	UBERON:0001388	98.30	gold quality
lower esophagus	UBERON:0013473	98.30	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.30	gold quality
left adrenal gland	UBERON:0001234	98.29	gold quality
left adrenal gland cortex	UBERON:0035825	98.27	gold quality
right adrenal gland cortex	UBERON:0035827	98.26	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	57.51
E-CURD-122	yes	17.15
E-ANND-3	yes	13.75
E-MTAB-9801	yes	7.27
E-MTAB-8410	yes	3.89
E-ENAD-17	no	891.84
E-CURD-112	no	19.89

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MTA1

Literature-anchored findings (GeneRIF, showing 17)

• Biogenesis of Lysosome-related Organelles complex-1 (BLOC-1) subunit 1 (BLOS1). (PMID:15102850)
• Together this study data provide evidence for the involvement of the BLOC-1 protein complex in SZ pathogenesis. (PMID:17618940)
• Experimental investigation of five specific genes, AP3B1, ATP6AP1, BLOC1S1, LAMP2, and RAB11A, has confirmed novel roles for these proteins in the proper initiation of macroautophagy in amino acid-starved fibroblasts. (PMID:19246570)
• GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain targets and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics (PMID:22309213)
• GCN5L1/BLOC1S1 regulates lysine acetylation in mitochondria. (PMID:22309213)
• Quantitative proteomic studies expand the functional repertoire of the BLOC-1 complex and provide insight into putative molecular pathways of schizophrenia susceptibility. (PMID:22423091)
• BLOS1 interacts with KXD1. (PMID:22554196)
• The Hermansky-Pudlak syndrome complex BLOC-1 and its cargo PI4KIIalpha interact with regulators of the actin cytoskeleton. (PMID:23676666)
• Using cancer cell lines, the study shows that BLOC1S1 mRNA is specifically cleaved by IRE1 at guanine 444, but only under conditions of IRE1 hyperactivation. (PMID:25870107)
• The interactions of GCN5L1, RanBP2 and alphaTAT1 function in concert to control alpha-tubulin acetylation and may contribute towards the regulation of cellular lysosome positioning. (PMID:30333138)
• Deletion of GCN5L1 in cardiomyocytes resulted in impaired myocardial post-ischemic function and increased infarct development. (PMID:30776374)
• The authors concluded that GCN5L1 increases lipotoxicity and epithelial-mesenchymal transition by promoting acetylation of LCAD (long-chain acyl-CoA dehydrogenase) and beta-HAD (beta-hydroxyacyl-CoA dehydrogenase). (PMID:31760589)
• General Control of Amino Acid Synthesis 5-Like 1-Mediated Acetylation of Manganese Superoxide Dismutase Regulates Oxidative Stress in Diabetic Kidney Disease. (PMID:33680286)
• A BLOC-1-AP-3 super-complex sorts a cis-SNARE complex into endosome-derived tubular transport carriers. (PMID:33886957)
• Mitochondrial GCN5L1 regulates glutaminase acetylation and hepatocellular carcinoma. (PMID:35538890)
• The endo-lysosomal regulatory protein BLOC1S1 modulates hepatic lysosomal content and lysosomal lipolysis. (PMID:36535215)
• GCN5L1-mediated acetylation prevents Rictor degradation in cardiac cells after hypoxic stress. (PMID:38281616)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bloc1s1	ENSDARG00000014171
mus_musculus	Bloc1s1	ENSMUSG00000090247
drosophila_melanogaster	Blos1	FBGN0050077
caenorhabditis_elegans		WBGENE00011872

Protein

Protein identifiers

Biogenesis of lysosome-related organelles complex 1 subunit 1 — P78537 (reviewed: P78537)

Alternative names: GCN5-like protein 1, Protein RT14, Protein acetyltransferase BLOC1S1

All UniProt accessions (5): P78537, F8VP73, F8W606, G8JLQ3, H0YHA4

UniProt curated annotations — full annotation on UniProt →

Function. Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. The BLOC-1 complex, in association with SNARE proteins, is also proposed to be involved in neurite extension. As part of the BORC complex may play a role in lysosomes movement and localization at the cell periphery. Associated with the cytosolic face of lysosomes, the BORC complex may recruit ARL8B and couple lysosomes to microtubule plus-end-directed kinesin motor. Acts as a protein acetyltransferase. Negatively regulates aerobic respiration through mitochondrial protein lysine-acetylation. May counteract the action of the deacetylase SIRT3 by acetylating and regulating proteins of the mitochondrial respiratory chain including ATP5F1A and NDUFA9. Acts as a regulator of mTORC2 signaling in response to hypotoxic stress by mediating acetylation of RICTOR, thereby protecting RICTOR against ubiquitination and subsequent degradation by the proteasome.

Subunit / interactions. Component of the biogenesis of lysosome-related organelles complex 1 (BLOC-1) composed of BLOC1S1, BLOC1S2, BLOC1S3, BLOC1S4, BLOC1S5, BLOC1S6, DTNBP1/BLOC1S7 and SNAPIN/BLOC1S8. Octamer composed of one copy each BLOC1S1, BLOC1S2, BLOC1S3, BLOC1S4, BLOC1S5, BLOC1S6, DTNBP1/BLOC1S7 and SNAPIN/BLOC1S8. The BLOC-1 complex associates with the AP-3 protein complex and membrane protein cargos. Component of the BLOC-one-related complex (BORC) which is composed of BLOC1S1, BLOC1S2, BORCS5, BORCS6, BORCS7, BORCS8, KXD1 and SNAPIN. Interacts with ATP5F1A and NDUFA9; involved in their acetylation on lysine residues. Interacts with KXD1.

Subcellular location. Mitochondrion intermembrane space. Mitochondrion matrix. Cytoplasm. Cytosol. Lysosome membrane.

Miscellaneous. May be produced by alternative initiation at Met-27 of isoform 1. A polymorphism at position 9 leads to the creation of a stop codon. Isoform 2 is the only form that exists in orthologs (except primates).

Similarity. Belongs to the BLOC1S1 family.

Isoforms (2)

UniProt ID	Names	Canonical?
P78537-1	1	yes
P78537-2	2

RefSeq proteins (1): NP_001478* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009395	BLOC1S1	Family

Pfam: PF06320

Catalyzed reactions (Rhea), 1 shown:

• L-lysyl-[protein] + acetyl-CoA = N(6)-acetyl-L-lysyl-[protein] + CoA + H(+) (RHEA:45948)

UniProt features (5 total): chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P78537-F1	89.59	0.78

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-432720	Lysosome Vesicle Biogenesis
R-HSA-432722	Golgi Associated Vesicle Biogenesis
R-HSA-199991	Membrane Trafficking
R-HSA-199992	trans-Golgi Network Vesicle Budding
R-HSA-5653656	Vesicle-mediated transport

MSigDB gene sets: 234 (showing top): GOBP_SYNAPTIC_VESICLE_LOCALIZATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_AXO_DENDRITIC_TRANSPORT, GOBP_VESICLE_LOCALIZATION, GOCC_VACUOLAR_MEMBRANE, MODULE_151, GOBP_VESICLE_ORGANIZATION, GOBP_SYNAPTIC_VESICLE_CYTOSKELETAL_TRANSPORT, GOBP_CELLULAR_PIGMENTATION, GOBP_NEUROGENESIS, RACCACAR_AML_Q6, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_ORGANELLE_TRANSPORT_ALONG_MICROTUBULE, SRF_Q5_01

GO Biological Process (12): anterograde axonal transport (GO:0008089), aerobic respiration (GO:0009060), endosomal transport (GO:0016197), peptidyl-lysine acetylation (GO:0018394), neuron projection development (GO:0031175), lysosome localization (GO:0032418), melanosome organization (GO:0032438), anterograde synaptic vesicle transport (GO:0048490), regulation of endosome size (GO:0051036), platelet dense granule organization (GO:0060155), regulation of lysosome size (GO:0062196), organelle transport along microtubule (GO:0072384)

GO Molecular Function (3): protein-lysine-acetyltransferase activity (GO:0061733), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (14): obsolete extracellular space (GO:0005615), mitochondrial intermembrane space (GO:0005758), mitochondrial matrix (GO:0005759), lysosomal membrane (GO:0005765), early endosome (GO:0005769), cytosol (GO:0005829), BLOC-1 complex (GO:0031083), cytoplasmic side of lysosomal membrane (GO:0098574), BORC complex (GO:0099078), axon cytoplasm (GO:1904115), cytoplasm (GO:0005737), mitochondrion (GO:0005739), lysosome (GO:0005764), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
trans-Golgi Network Vesicle Budding	2
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoplasm	2
axonal transport	1
axon cytoplasm	1
cellular respiration	1
vesicle-mediated transport	1
intracellular transport	1
protein acetylation	1
peptidyl-lysine modification	1
neuron development	1
plasma membrane bounded cell projection organization	1
vacuolar localization	1
pigment granule organization	1
anterograde axonal transport	1
synaptic vesicle transport along microtubule	1
regulation of vesicle size	1
secretory granule organization	1
regulation of cellular component size	1
transport along microtubule	1
establishment of organelle localization	1
protein N-acetyltransferase activity	1
binding	1
catalytic activity	1
mitochondrial envelope	1
organelle envelope lumen	1
mitochondrion	1
intracellular organelle lumen	1
lysosome	1
lytic vacuole membrane	1
endosome	1
BLOC complex	1
lysosomal membrane	1
cytoplasmic side of membrane	1
intracellular protein-containing complex	1
axon	1
neuron projection cytoplasm	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1
lytic vacuole	1

Protein interactions and networks

STRING

1130 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BLOC1S1	SNAPIN	O95295	999
BLOC1S1	BLOC1S2	Q6QNY1	999
BLOC1S1	BLOC1S3	Q6QNY0	999
BLOC1S1	BLOC1S6	Q9UL45	999
BLOC1S1	DTNBP1	Q96EV8	993
BLOC1S1	KXD1	Q9BQD3	991
BLOC1S1	BORCS6	Q96GS4	986
BLOC1S1	BORCS5	Q969J3	985
BLOC1S1	BORCS8	Q96FH0	975
BLOC1S1	BORCS7	Q96B45	966
BLOC1S1	BLOC1S4	Q9NUP1	916
BLOC1S1	BLOC1S5	Q8TDH9	855
BLOC1S1	KAT2A	Q92830	646
BLOC1S1	HPS6	Q86YV9	639
BLOC1S1	KAT2B	Q92831	617

IntAct

90 interactions, top by confidence:

A	B	Type	Score
LAMTOR4	LAMTOR5	psi-mi:“MI:0914”(association)	0.960
DTNBP1	SNAPIN	psi-mi:“MI:0914”(association)	0.900
BLOC1S1	BLOC1S6	psi-mi:“MI:0915”(physical association)	0.890
BLOC1S6	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.890
BLOC1S6	BLOC1S1	psi-mi:“MI:0914”(association)	0.890
BLOC1S2	SNAPIN	psi-mi:“MI:0914”(association)	0.830
SNAPIN	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.810
BLOC1S1	SNAPIN	psi-mi:“MI:0914”(association)	0.810
BLOC1S1	SNAPIN	psi-mi:“MI:0915”(physical association)	0.810
BLOC1S1	BLOC1S2	psi-mi:“MI:0915”(physical association)	0.700
FAM9C	NDC80	psi-mi:“MI:0914”(association)	0.670
BLOC1S1	BLOC1S4	psi-mi:“MI:0914”(association)	0.660
BLOC1S1	BLOC1S4	psi-mi:“MI:0915”(physical association)	0.660
BLOC1S6	SNAPIN	psi-mi:“MI:0914”(association)	0.640
FBXO44	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.560
DCTN2	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.560
HGS	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.560
USHBP1	BLOC1S1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (88): BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), CLTC (Co-fractionation), BLOC1S1 (Synthetic Growth Defect), BLOC1S1 (Synthetic Growth Defect), BLOC1S1 (Proximity Label-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS), BLOC1S1 (Affinity Capture-MS)

ESM2 similar proteins: A4FUD6, B5KFI0, D3ZKU7, O43752, O55102, O75486, P60228, P60229, P78537, Q05AY2, Q05B58, Q08DP2, Q08DU8, Q0VFD8, Q1LUA8, Q2NKW0, Q32L03, Q32WR5, Q3B8M3, Q3SZ60, Q3T102, Q4R6G8, Q4R7C8, Q5R6Q2, Q5R7L8, Q5R8K9, Q5R8N4, Q5ZJA9, Q5ZL19, Q5ZLA5, Q63635, Q641X8, Q66KB9, Q6I9Y2, Q6P643, Q6P7L9, Q6QNY1, Q7SZ78, Q7TMY4, Q7Z3J2

Diamond homologs: A1Z9S1, D3ZKU7, O22929, O55102, P78537, Q0VFD8, Q22616, Q2NKW0, Q54VX7, Q5R7L8

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
BLOC1S1	“form complex”	BLOC-1	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 63 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
trans-Golgi Network Vesicle Budding	6	40.1×	2e-06
Golgi Associated Vesicle Biogenesis	6	31.6×	4e-06

GO biological processes:

GO term	Partners	Fold	FDR
anterograde synaptic vesicle transport	8	146.9×	7e-14
melanosome organization	8	96.0×	2e-12
anterograde axonal transport	8	86.1×	4e-12
lysosome localization	6	58.5×	5e-08
neuron projection development	7	15.8×	2e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

784 predictions. Top by Δscore:

Variant	Effect	Δscore
12:55716195:GG:G	donor_gain	1.0000
12:55716196:GG:G	donor_gain	1.0000
12:55719081:A:AG	acceptor_gain	1.0000
12:55719082:A:G	acceptor_gain	1.0000
12:55719086:CCCA:C	acceptor_loss	1.0000
12:55719087:CCA:C	acceptor_loss	1.0000
12:55719089:A:AG	acceptor_gain	1.0000
12:55719089:AGT:A	acceptor_gain	1.0000
12:55719089:AGTGT:A	acceptor_gain	1.0000
12:55719090:G:GT	acceptor_gain	1.0000
12:55719090:GT:G	acceptor_gain	1.0000
12:55719090:GTG:G	acceptor_gain	1.0000
12:55719090:GTGT:G	acceptor_gain	1.0000
12:55719090:GTGTG:G	acceptor_gain	1.0000
12:55719220:CAAG:C	donor_loss	1.0000
12:55719221:AAG:A	donor_loss	1.0000
12:55719224:GT:G	donor_loss	1.0000
12:55719585:G:T	donor_gain	1.0000
12:55716192:GCAGG:G	donor_gain	0.9900
12:55716197:G:C	donor_loss	0.9900
12:55716197:G:GG	donor_gain	0.9900
12:55716198:T:A	donor_loss	0.9900
12:55716198:T:G	donor_loss	0.9900
12:55716269:G:GG	donor_gain	0.9900
12:55716288:G:T	donor_gain	0.9900
12:55716931:A:AG	acceptor_gain	0.9900
12:55716932:G:GG	acceptor_gain	0.9900
12:55717001:GTGGG:G	donor_gain	0.9900
12:55717003:GGGGT:G	donor_loss	0.9900
12:55717005:GGT:G	donor_loss	0.9900

AlphaMissense

998 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:55716950:G:C	A55P	1.000
12:55716996:T:C	L70P	1.000
12:55719114:A:C	Q81P	1.000
12:55719144:T:C	L91P	1.000
12:55719155:G:C	A95P	1.000
12:55719185:T:A	W105R	1.000
12:55719185:T:C	W105R	1.000
12:55719187:G:C	W105C	1.000
12:55719187:G:T	W105C	1.000
12:55719215:G:C	A115P	1.000
12:55719219:T:A	L116H	1.000
12:55719219:T:C	L116P	1.000
12:55719223:G:C	K117N	1.000
12:55719223:G:T	K117N	1.000
12:55719505:G:A	G120R	1.000
12:55719505:G:C	G120R	1.000
12:55719506:G:A	G120E	1.000
12:55719506:G:T	G120V	1.000
12:55719520:T:A	W125R	1.000
12:55719520:T:C	W125R	1.000
12:55719522:G:C	W125C	1.000
12:55719522:G:T	W125C	1.000
12:55719523:G:C	A126P	1.000
12:55719524:C:A	A126D	1.000
12:55719556:G:C	A137P	1.000
12:55716959:G:C	A58P	0.999
12:55716962:G:C	A59P	0.999
12:55716963:C:A	A59E	0.999
12:55716972:T:C	L62P	0.999
12:55716996:T:A	L70H	0.999

dbSNP variants (sampled 300 via entrez): RS1000187510 (12:55717855 G>A), RS1001011850 (12:55716436 C>T), RS1002161774 (12:55718333 C>T), RS1002165810 (12:55715971 A>G), RS1002603694 (12:55719753 A>G), RS1002657866 (12:55719440 G>A,C), RS1002770957 (12:55719981 A>G), RS1003100626 (12:55719673 A>G,T), RS1003791328 (12:55714238 C>G,T), RS1004073136 (12:55715561 C>T), RS1005040363 (12:55718622 G>T), RS1005339269 (12:55718370 G>A), RS1006751096 (12:55720042 C>T), RS1007133085 (12:55719894 T>C), RS1007391283 (12:55714462 G>A)

Disease associations

OMIM: gene MIM:601444 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
neurodevelopmental disorder	Strong	Autosomal recessive
complex neurodevelopmental disorder	Limited	Autosomal recessive

Mondo (2): complex neurodevelopmental disorder (MONDO:0100038), neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST010002_217	Refractive error	6.000000e-174

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
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

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases reaction, increases expression, affects expression, affects binding	3
Estradiol	increases reaction, decreases expression, affects binding	3
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	decreases phosphorylation	1
triphenyl phosphate	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
cupric oxide	increases expression	1
pentabromodiphenyl ether	decreases expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
14-deoxy-11,12-didehydroandrographolide	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
bisphenol S	decreases reaction, affects binding	1
jinfukang	increases expression	1
bisphenol AF	affects binding, decreases reaction	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Bilirubin	decreases expression	1
Diethylstilbestrol	decreases expression	1
Smoke	decreases expression	1
Tretinoin	increases expression	1
Tunicamycin	decreases expression	1
Valproic Acid	decreases expression, decreases methylation	1
Cyproterone Acetate	affects binding, affects folding, increases reaction	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

7 cell lines: 6 induced pluripotent stem cell, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1LB	Abcam HeLa BLOC1S1 KO	Cancer cell line	Female
CVCL_B7SV	NIHTVBi019-A	Induced pluripotent stem cell	Female
CVCL_B7SW	NIHTVBi019-A-1	Induced pluripotent stem cell	Female
CVCL_B7SX	NIHTVBi020-A	Induced pluripotent stem cell	Female
CVCL_B7SY	NIHTVBi021-A	Induced pluripotent stem cell	Male
CVCL_B7SZ	NIHTVBi022-A	Induced pluripotent stem cell	Male
CVCL_E4P1	KOLF2.1J BLOC1S1 3.7kbdel DEL/DEL	Induced pluripotent stem cell	Male

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
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
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