SSBP3

Summary

SSBP3 (single stranded DNA binding protein 3, HGNC:15674) is a protein-coding gene on chromosome 1p32.3, encoding Single-stranded DNA-binding protein 3 (Q9BWW4). May be involved in transcription regulation of the alpha 2(I) collagen gene where it binds to the single-stranded polypyrimidine sequences in the promoter region. It is a selective cancer dependency (DepMap: 36.8% of cell lines).

Predicted to enable single-stranded DNA binding activity and transcription coactivator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within hematopoietic progenitor cell differentiation. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus.

Source: NCBI Gene 23648 — RefSeq curated summary.

At a glance

• GWAS associations: 57
• Clinical variants (ClinVar): 73 total
• Cancer dependency (DepMap): dependent in 36.8% of screened cell lines
• MANE Select transcript: NM_145716

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15674
Approved symbol	SSBP3
Name	single stranded DNA binding protein 3
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	CSDP, SSDP, FLJ10355, SSDP1
Ensembl gene	ENSG00000157216
Ensembl biotype	protein_coding
OMIM	607390
Entrez	23648

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 10 protein_coding, 5 protein_coding_CDS_not_defined, 5 retained_intron

ENST00000326956, ENST00000357475, ENST00000371319, ENST00000371320, ENST00000417664, ENST00000420121, ENST00000426150, ENST00000444533, ENST00000448572, ENST00000525990, ENST00000528787, ENST00000528930, ENST00000530618, ENST00000533209, ENST00000533946, ENST00000610401, ENST00000909144, ENST00000909145, ENST00000936591, ENST00000936592

RefSeq mRNA: 11 — MANE Select: NM_145716 NM_001009955, NM_001394360, NM_001394361, NM_001394362, NM_001394363, NM_001394364, NM_001394365, NM_001394366, NM_001394367, NM_018070, NM_145716

CCDS: CCDS30726, CCDS590, CCDS591, CCDS90961

Canonical transcript exons

ENST00000610401 — 18 exons

Exon	Start	End
ENSE00001454935	54405953	54406394
ENSE00003510190	54240905	54240959
ENSE00003560019	54281438	54281527
ENSE00003564214	54239129	54239199
ENSE00003570375	54243235	54243299
ENSE00003570464	54404858	54404930
ENSE00003621116	54228449	54228477
ENSE00003627564	54404576	54404637
ENSE00003628092	54251794	54251860
ENSE00003629596	54257127	54257186
ENSE00003633667	54258069	54258149
ENSE00003653758	54228748	54228826
ENSE00003655596	54251616	54251692
ENSE00003676565	54401861	54401945
ENSE00003679970	54228255	54228356
ENSE00003680272	54241474	54241509
ENSE00003693762	54242164	54242212
ENSE00003718240	54225432	54227160

Expression profiles

Bgee: expression breadth ubiquitous, 266 present calls, max score 99.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.3686 / max 127.9761, expressed in 1809 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12467	15.5183	1786
12469	1.2978	580
12463	1.2550	601
12462	0.2339	134
12468	0.0324	10
12461	0.0313	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	99.30	gold quality
left ovary	UBERON:0002119	97.88	gold quality
popliteal artery	UBERON:0002250	97.72	gold quality
tibial artery	UBERON:0007610	97.72	gold quality
right ovary	UBERON:0002118	97.46	gold quality
prefrontal cortex	UBERON:0000451	97.36	gold quality
cingulate cortex	UBERON:0003027	97.24	gold quality
anterior cingulate cortex	UBERON:0009835	97.24	gold quality
ovary	UBERON:0000992	97.13	gold quality
right frontal lobe	UBERON:0002810	97.05	gold quality
endocervix	UBERON:0000458	97.04	gold quality
ectocervix	UBERON:0012249	96.81	gold quality
right coronary artery	UBERON:0001625	96.74	gold quality
neocortex	UBERON:0001950	96.70	gold quality
body of uterus	UBERON:0009853	96.69	gold quality
cerebellar hemisphere	UBERON:0002245	96.59	gold quality
frontal cortex	UBERON:0001870	96.52	gold quality
ventricular zone	UBERON:0003053	96.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.52	gold quality
cerebellar cortex	UBERON:0002129	96.50	gold quality
aorta	UBERON:0000947	96.45	gold quality
primary visual cortex	UBERON:0002436	96.43	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.31	gold quality
body of stomach	UBERON:0001161	96.28	gold quality
ganglionic eminence	UBERON:0004023	96.20	gold quality
Brodmann (1909) area 9	UBERON:0013540	96.16	gold quality
left coronary artery	UBERON:0001626	96.14	gold quality
granulocyte	CL:0000094	95.96	gold quality
cerebellum	UBERON:0002037	95.96	gold quality
mucosa of stomach	UBERON:0001199	95.94	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-109979	yes	240.76
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SMAD5

miRNA regulators (miRDB)

84 targeting SSBP3, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4447	99.85	67.81	2900
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-6505-5P	99.73	69.25	1595

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 36.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

• Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development (PMID:12381786)
• Thus, biochemical data of SSDP1 presented by this study provides biochemical evidence for a better understanding of transcriptional regulation. (PMID:16325762)
• phosphorylation involving N-terminal tyrosine residues of Ssdp1 is a means of regulating its nuclear localization and subsequent transcriptional activation of LIM-HD complexes. (PMID:18080319)
• SSBP3 Interacts With Islet-1 and Ldb1 to Impact Pancreatic beta-Cell Target Genes (PMID:26495868)
• SIVA1 enhances SSBP3 ubiquitination and promotes SSBP3 protein turnover (PMID:30363057)
• The SSBP3 co-regulator is required for glucose homeostasis, pancreatic islet architecture, and beta-cell identity. (PMID:37536498)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	ssbp3b	ENSDARG00000030155
danio_rerio	ssbp3a	ENSDARG00000058237
mus_musculus	Ssbp3	ENSMUSG00000061887
rattus_norvegicus	Ssbp3	ENSRNOG00000007920
drosophila_melanogaster	Ssdp	FBGN0011481
caenorhabditis_elegans		WBGENE00012990
caenorhabditis_elegans		WBGENE00013152

Paralogs (2): SSBP4 (ENSG00000130511), SSBP2 (ENSG00000145687)

Protein

Protein identifiers

Single-stranded DNA-binding protein 3 — Q9BWW4 (reviewed: Q9BWW4)

Alternative names: Sequence-specific single-stranded-DNA-binding protein

All UniProt accessions (5): Q9BWW4, A0A087WVT6, E9PK49, Q5T863, Q9NW25

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcription regulation of the alpha 2(I) collagen gene where it binds to the single-stranded polypyrimidine sequences in the promoter region.

Subcellular location. Nucleus.

Tissue specificity. Highly expressed in all hematopoietic tissues, including spleen, lymph node, peripheral blood, bone marrow, thymus, and fetal liver, with highest expression in thymus and fetal liver. Expression is also high in heart, brain, kidney, and skeletal muscle.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9BWW4-1	1	yes
Q9BWW4-2	2
Q9BWW4-3	3

RefSeq proteins (11): NP_001009955, NP_001381289, NP_001381290, NP_001381291, NP_001381292, NP_001381293, NP_001381294, NP_001381295, NP_001381296, NP_060540, NP_663768* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006594	LisH	Conserved_site
IPR008116	SSDP_DNA-bd	Family

Pfam: PF04503

UniProt features (23 total): modified residue 10, compositionally biased region 8, splice variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWW4-F1	55.71	0.15

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 (10): 1, 155, 161, 165, 347, 352, 355, 360, 381, 387

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 249 (showing top): FXR_IR1_Q6, GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_BODY_MORPHOGENESIS, AREB6_03, MAZ_Q6, GOBP_NEURAL_TUBE_DEVELOPMENT, FOXO4_01, FOXO1_01, GGGTGGRR_PAX4_03, AACWWCAANK_UNKNOWN, NKX61_01, E2F_Q3, SOX9_B1

GO Biological Process (11): hematopoietic progenitor cell differentiation (GO:0002244), positive regulation of cell population proliferation (GO:0008284), prechordal plate formation (GO:0021501), midbrain-hindbrain boundary initiation (GO:0021547), positive regulation of transcription by RNA polymerase II (GO:0045944), mesendoderm development (GO:0048382), head morphogenesis (GO:0060323), protein-containing complex assembly (GO:0065003), positive regulation of anterior head development (GO:2000744), positive regulation of DNA-templated transcription (GO:0045893), head development (GO:0060322)

GO Molecular Function (4): single-stranded DNA binding (GO:0003697), transcription coactivator activity (GO:0003713), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), transcription regulator complex (GO:0005667), protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of DNA-templated transcription	2
anatomical structure development	2
hemopoiesis	1
cell differentiation	1
cell population proliferation	1
regulation of cell population proliferation	1
positive regulation of cellular process	1
nervous system development	1
anatomical structure formation involved in morphogenesis	1
regionalization	1
neural plate anterior/posterior regionalization	1
midbrain-hindbrain boundary development	1
formation of anatomical boundary	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
endoderm development	1
mesoderm development	1
anatomical structure morphogenesis	1
body morphogenesis	1
head development	1
cellular component assembly	1
protein-containing complex organization	1
positive regulation of developmental process	1
anterior head development	1
regulation of anterior head development	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
DNA binding	1
transcription coregulator activity	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
protein-containing complex	1
cellular_component	1

Protein interactions and networks

STRING

544 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SSBP3	LDB1	Q86U70	835
SSBP3	LDB2	O43679	786
SSBP3	LMO2	P25791	609
SSBP3	LHX3	Q9UBR4	575
SSBP3	RLIM	Q9NVW2	513
SSBP3	SSBP1	Q04837	492
SSBP3	INIP	Q9NRY2	470
SSBP3	RNF20	Q5VTR2	448
SSBP3	GATA1	P15976	442
SSBP3	TAL1	P17542	439
SSBP3	BCL9	O00512	438
SSBP3	LACTBL1	A8MY62	432
SSBP3	LMNA	P02545	422
SSBP3	ZFPM1	Q8IX07	414
SSBP3	SSBP2	P81877	411

IntAct

142 interactions, top by confidence:

A	B	Type	Score
LMO1	ZBTB43	psi-mi:“MI:0914”(association)	0.830
SSBP3	LDB1	psi-mi:“MI:0915”(physical association)	0.740
LMX1B	SSBP3	psi-mi:“MI:0915”(physical association)	0.740
SSBP3	LMX1B	psi-mi:“MI:0914”(association)	0.740
YES1	SSBP3	psi-mi:“MI:0915”(physical association)	0.720
PIN1	SSBP3	psi-mi:“MI:0915”(physical association)	0.720
IL36RN	SSBP3	psi-mi:“MI:0915”(physical association)	0.720
SSBP3	YES1	psi-mi:“MI:0915”(physical association)	0.720
SSBP3	IL36RN	psi-mi:“MI:0915”(physical association)	0.720
PYGO1	BCL9	psi-mi:“MI:0914”(association)	0.700
LHX8	LDB1	psi-mi:“MI:0914”(association)	0.690
SSBP3	LHX1	psi-mi:“MI:0914”(association)	0.570
LHX3	LDB1	psi-mi:“MI:0914”(association)	0.570
SSBP3	EWSR1	psi-mi:“MI:0915”(physical association)	0.560
SSBP3	NXT2	psi-mi:“MI:0915”(physical association)	0.560
SSBP3	TBC1D23	psi-mi:“MI:0915”(physical association)	0.560
TBC1D23	SSBP3	psi-mi:“MI:0915”(physical association)	0.560
EWSR1	SSBP3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (172): SSBP3 (Two-hybrid), SSBP3 (Two-hybrid), SSBP3 (Two-hybrid), SSBP3 (Two-hybrid), SSBP3 (Two-hybrid), IL36RN (Two-hybrid), TBC1D23 (Two-hybrid), NXT2 (Two-hybrid), SSBP3 (Affinity Capture-MS), SSBP3 (Affinity Capture-MS), SSBP3 (Affinity Capture-MS), SSBP3 (Affinity Capture-MS), LDB1 (Affinity Capture-MS), DIS3 (Affinity Capture-MS), LHX1 (Affinity Capture-MS)

ESM2 similar proteins: A1YFU7, A2AJK6, A2YWA6, A2Z259, A5HEH4, A8WL06, A9YDN6, B7FAS6, E3KIY6, G4MWZ7, G5ED29, G5EEL0, H2KZZ2, O14770, O35740, P18488, P25822, P34545, P81877, P97367, Q03372, Q06A37, Q0VCT9, Q10666, Q21955, Q24533, Q24573, Q29A33, Q2MJT0, Q59QW5, Q60YF6, Q61L47, Q67FY3, Q6YXH5, Q6ZB90, Q7SAX8, Q92258, Q93VH6, Q98948, Q99967

Diamond homologs: B7FAS6, P81877, Q98948, Q9BWG4, Q9BWW4, Q9CYZ8, Q9D032, Q9R050, A0AUS0, A1CUD6, A6ZR64, A7RHG8, A7YY75, B2AEZ5, B3LRM5, B5VHN4, B6GZD3, B6HP56, B6QC06, B8N9H4, B9WD30, C0S902, C1BK83, C1GB49, C4JPW9, C7GS77, C8Z7C7, D5GBI7, O14186, O22212, O35828, O48847, O74184, P0CS38, P0CS39, P40068, P74598, P87314, Q05BV3, Q06440

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
LCK	“up-regulates activity”	SSBP3	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 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.

GO biological processes:

GO term	Partners	Fold	FDR
neuron fate specification	5	38.6×	2e-05
neuron differentiation	14	15.4×	1e-10
somatic stem cell population maintenance	5	13.6×	2e-03
transcription by RNA polymerase II	8	6.2×	2e-03
brain development	7	6.1×	7e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	42
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3992 predictions. Top by Δscore:

Variant	Effect	Δscore
1:54228253:A:AC	donor_gain	1.0000
1:54228254:C:CC	donor_gain	1.0000
1:54228254:CA:C	donor_gain	1.0000
1:54228352:GAATT:G	acceptor_gain	1.0000
1:54228353:AATT:A	acceptor_gain	1.0000
1:54228354:ATT:A	acceptor_gain	1.0000
1:54228354:ATTC:A	acceptor_loss	1.0000
1:54228355:TT:T	acceptor_gain	1.0000
1:54228355:TTCT:T	acceptor_loss	1.0000
1:54228356:TC:T	acceptor_loss	1.0000
1:54228357:C:CC	acceptor_gain	1.0000
1:54228357:C:G	acceptor_loss	1.0000
1:54228447:A:AC	donor_gain	1.0000
1:54228448:C:CA	donor_gain	1.0000
1:54228448:CT:C	donor_gain	1.0000
1:54228448:CTT:C	donor_gain	1.0000
1:54228827:C:CC	acceptor_gain	1.0000
1:54239123:ACTT:A	donor_loss	1.0000
1:54239124:CTT:C	donor_loss	1.0000
1:54239125:TTA:T	donor_loss	1.0000
1:54239126:T:TG	donor_loss	1.0000
1:54239127:A:AC	donor_gain	1.0000
1:54239127:AC:A	donor_loss	1.0000
1:54239128:C:CG	donor_gain	1.0000
1:54239128:CG:C	donor_gain	1.0000
1:54239209:A:T	acceptor_gain	1.0000
1:54240899:TCTTA:T	donor_loss	1.0000
1:54240900:CTTAC:C	donor_loss	1.0000
1:54240901:TTAC:T	donor_loss	1.0000
1:54240902:TACC:T	donor_loss	1.0000

AlphaMissense

2347 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:54401866:C:G	D91H	1.000
1:54401870:A:C	F89L	1.000
1:54401870:A:T	F89L	1.000
1:54401871:A:C	F89C	1.000
1:54401871:A:G	F89S	1.000
1:54401872:A:C	F89V	1.000
1:54401872:A:G	F89L	1.000
1:54401872:A:T	F89I	1.000
1:54401876:T:A	K87N	1.000
1:54401876:T:G	K87N	1.000
1:54401881:C:G	A86P	1.000
1:54401884:C:T	E85K	1.000
1:54401906:T:A	R77S	1.000
1:54401906:T:G	R77S	1.000
1:54401907:C:A	R77I	1.000
1:54401907:C:G	R77T	1.000
1:54401909:C:A	R76S	1.000
1:54401909:C:G	R76S	1.000
1:54401910:C:A	R76M	1.000
1:54401910:C:G	R76T	1.000
1:54401922:G:T	A72E	1.000
1:54401923:C:G	A72P	1.000
1:54401924:A:C	C71W	1.000
1:54401925:C:T	C71Y	1.000
1:54401926:A:G	C71R	1.000
1:54401929:A:C	Y70D	1.000
1:54401929:A:G	Y70H	1.000
1:54401929:A:T	Y70N	1.000
1:54401931:A:C	L69R	1.000
1:54401931:A:G	L69P	1.000

dbSNP variants (sampled 300 via entrez): RS1000016002 (1:54394954 C>G,T), RS1000024669 (1:54240177 G>A), RS1000032209 (1:54283237 C>T), RS1000038275 (1:54245596 A>T), RS1000044496 (1:54349253 A>G), RS1000047009 (1:54228821 C>T), RS1000050737 (1:54280420 C>A), RS1000068862 (1:54249022 T>C), RS1000086775 (1:54388810 T>C), RS1000087222 (1:54383879 G>C), RS1000091572 (1:54245879 G>A), RS1000106813 (1:54283541 T>G), RS1000126717 (1:54243912 C>A,T), RS1000139962 (1:54352217 A>G), RS1000153793 (1:54254063 G>A)

Disease associations

OMIM: gene MIM:607390 | disease phenotypes:

GenCC curated gene-disease

Mondo (2): neurodevelopmental disorder (MONDO:0700092), syndromic intellectual disability (MONDO:0000508)

Orphanet (1): Rare genetic syndromic intellectual disability (Orphanet:183763)

HPO phenotypes

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

GWAS associations

57 associations (top):

Study	Trait	p-value
GCST002783_357	Body mass index	4.000000e-06
GCST002790_1	Food allergy	3.000000e-07
GCST003993_2	Menarche (age at onset)	1.000000e-08
GCST004616_107	Platelet distribution width	2.000000e-09
GCST004826_13	P wave duration	3.000000e-09
GCST004826_2	P wave duration	2.000000e-08
GCST005986_2	Blood urea nitrogen levels	7.000000e-11
GCST007018_9	Serum bilirubin levels in metabolic syndrome	7.000000e-06
GCST008062_74	Blood urea nitrogen levels	8.000000e-14
GCST009017_1	T wave morphology restitution during recovery from exercise (MTAG)	2.000000e-08
GCST009069_1	T wave morphology restitution during recovery from exercise	4.000000e-08
GCST010002_385	Refractive error	7.000000e-13
GCST010173_90	Triglyceride levels	1.000000e-10
GCST010244_337	Triglyceride levels	8.000000e-14
GCST010320_76	PR interval	1.000000e-09
GCST010321_174	PR interval	3.000000e-11
GCST010346_2	TPE interval (resting)	6.000000e-21
GCST010346_26	TPE interval (resting)	1.000000e-10
GCST010346_9	TPE interval (resting)	5.000000e-12
GCST010696_4	Cortical thickness (min-P)	1.000000e-08
GCST010697_20	Cortical surface area (min-P)	1.000000e-08
GCST010698_15	Subcortical volume (min-P)	8.000000e-09
GCST010699_85	Brain morphology (min-P)	3.000000e-14
GCST010700_4	Cortical thickness (MOSTest)	8.000000e-18
GCST010701_102	Cortical surface area (MOSTest)	2.000000e-12
GCST010702_88	Subcortical volume (MOSTest)	9.000000e-09
GCST010703_104	Brain morphology (MOSTest)	9.000000e-21
GCST010796_2338	Electrocardiogram morphology (amplitude at temporal datapoints)	4.000000e-27
GCST010796_2339	Electrocardiogram morphology (amplitude at temporal datapoints)	3.000000e-27
GCST010796_2340	Electrocardiogram morphology (amplitude at temporal datapoints)	6.000000e-28

EFO canonical traits (16, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0007016	food allergy measurement
EFO:0004703	age at menarche
EFO:0007984	platelet component distribution width
EFO:0005094	P wave duration
EFO:0004570	bilirubin measurement
EFO:0008398	T wave morphology measurement
EFO:0004530	triglyceride measurement
EFO:0004462	PR interval
EFO:0004644	TPE interval measurement
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0004327	electrocardiography
EFO:0009819	comparative body size at age 10, self-reported
EFO:0005091	monocyte count
EFO:0004533	alkaline phosphatase measurement

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

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, decreases methylation	5
bisphenol S	affects cotreatment, increases methylation, decreases methylation, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects methylation, affects cotreatment, decreases methylation	1
lead acetate	increases expression, affects cotreatment	1
arsenite	increases methylation	1
zinc protoporphyrin	affects cotreatment, increases expression	1
sodium arsenite	increases expression	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
NSC 689534	affects binding, decreases expression	1
Arsenic Trioxide	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation, increases methylation	1
Caffeine	affects phosphorylation	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methapyrilene	decreases methylation	1
Phthalic Acids	decreases methylation	1
Tobacco Smoke Pollution	decreases methylation	1
Tretinoin	decreases expression	1
Urethane	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2HE	Abcam HeLa SSBP3 KO	Cancer cell line	Female

Clinical trials (associated diseases)

202 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
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
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice