FOXP1

Summary

FOXP1 (forkhead box P1, HGNC:3823) is a protein-coding gene on chromosome 3p13, encoding Forkhead box protein P1 (Q9H334). Transcriptional repressor. It is haploinsufficient (ClinGen: sufficient evidence).

This gene belongs to subfamily P of the forkhead box (FOX) transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Forkhead box P1 protein contains both DNA-binding- and protein-protein binding-domains. This gene may act as a tumor suppressor as it is lost in several tumor types and maps to a chromosomal region (3p14.1) reported to contain a tumor suppressor gene(s). Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 27086 — RefSeq curated summary.

At a glance

• Gene–disease (curated): intellectual disability-severe speech delay-mild dysmorphism syndrome (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 112
• Clinical variants (ClinVar): 1,116 total — 132 pathogenic, 67 likely-pathogenic
• Phenotypes (HPO): 98
• Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 2 cancer types
• Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
• Transcription factor: yes — 38 downstream targets (CollecTRI)
• MANE Select transcript: NM_001349338

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3823
Approved symbol	FOXP1
Name	forkhead box P1
Location	3p13
Locus type	gene with protein product
Status	Approved
Aliases	QRF1, 12CC4, HSPC215, hFKH1B
Ensembl gene	ENSG00000114861
Ensembl biotype	protein_coding
OMIM	605515
Entrez	27086

Gene structure

Transcript identifiers

Ensembl transcripts: 145 — 110 protein_coding, 19 protein_coding_CDS_not_defined, 11 retained_intron, 5 nonsense_mediated_decay

ENST00000318779, ENST00000318789, ENST00000327590, ENST00000460805, ENST00000468577, ENST00000470112, ENST00000471386, ENST00000472382, ENST00000475937, ENST00000484350, ENST00000485326, ENST00000491238, ENST00000493010, ENST00000493089, ENST00000497355, ENST00000497553, ENST00000498215, ENST00000614176, ENST00000614183, ENST00000615603, ENST00000620572, ENST00000622151, ENST00000647614, ENST00000647649, ENST00000647741, ENST00000647776, ENST00000647829, ENST00000648107, ENST00000648113, ENST00000648155, ENST00000648192, ENST00000648321, ENST00000648380, ENST00000648384, ENST00000648426, ENST00000648654, ENST00000648662, ENST00000648710, ENST00000648718, ENST00000648748, ENST00000648783, ENST00000648794, ENST00000648826, ENST00000648895, ENST00000649081, ENST00000649133, ENST00000649145, ENST00000649175, ENST00000649328, ENST00000649417, ENST00000649431, ENST00000649439, ENST00000649513, ENST00000649528, ENST00000649592, ENST00000649596, ENST00000649610, ENST00000649631, ENST00000649659, ENST00000649695, ENST00000649760, ENST00000650068, ENST00000650073, ENST00000650156, ENST00000650188, ENST00000650231, ENST00000650295, ENST00000650387, ENST00000650402, ENST00000650555, ENST00000650580, ENST00000866054, ENST00000866055, ENST00000866056, ENST00000866057, ENST00000866058, ENST00000866059, ENST00000866060, ENST00000866061, ENST00000866062, ENST00000866063, ENST00000866064, ENST00000866065, ENST00000866066, ENST00000866067, ENST00000866068, ENST00000866069, ENST00000866070, ENST00000866071, ENST00000866072, ENST00000866073, ENST00000866074, ENST00000866075, ENST00000866076, ENST00000866077, ENST00000866078, ENST00000866079, ENST00000866080, ENST00000866081, ENST00000866082, ENST00000866083, ENST00000866084, ENST00000866085, ENST00000866086, ENST00000866087, ENST00000866088, ENST00000866089, ENST00000866090, ENST00000866091, ENST00000866092, ENST00000866093, ENST00000866094, ENST00000866095, ENST00000866096, ENST00000866097, ENST00000866098, ENST00000866099, ENST00000866100, ENST00000866101, ENST00000866102, ENST00000923826, ENST00000923827, ENST00000923828, ENST00000923829, ENST00000968296, ENST00000968297, ENST00000968298, ENST00000968299, ENST00000968300, ENST00000968301, ENST00000968302, ENST00000968303, ENST00000968304, ENST00000968305, ENST00000968306, ENST00000968307, ENST00000968308, ENST00000968309, ENST00000968310, ENST00000968311, ENST00000968312, ENST00000968313, ENST00000968314, ENST00000968315, ENST00000968316

RefSeq mRNA: 17 — MANE Select: NM_001349338 NM_001012505, NM_001244808, NM_001244810, NM_001244812, NM_001244813, NM_001244814, NM_001244815, NM_001244816, NM_001349337, NM_001349338, NM_001349340, NM_001349341, NM_001349342, NM_001349343, NM_001349344, NM_001370548, NM_032682

CCDS: CCDS2914, CCDS33785, CCDS58838, CCDS58839, CCDS74963, CCDS74964, CCDS93310, CCDS93311, CCDS93312

Canonical transcript exons

ENST00000649528 — 21 exons

Exon	Start	End
ENSE00000000332	70954708	70959391
ENSE00001002137	70987994	70988077
ENSE00001258538	71581549	71581697
ENSE00001258582	71359150	71359244
ENSE00001258595	71299820	71299880
ENSE00001258613	70977828	70978029
ENSE00001258621	71000972	71001059
ENSE00001411968	71493426	71493555
ENSE00002383297	70977643	70977722
ENSE00002387336	71112536	71112637
ENSE00002400196	70972555	70972676
ENSE00002417698	70976941	70977042
ENSE00002710535	71198202	71198392
ENSE00003478509	71053636	71053773
ENSE00003528753	70970736	70970805
ENSE00003655782	70965890	70966056
ENSE00003719412	71041328	71041532
ENSE00003722974	71046942	71047095
ENSE00003752337	71052537	71052626
ENSE00003790933	71015549	71015653
ENSE00003837660	71583571	71583728

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.86.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 70.1043 / max 1737.5509, expressed in 1809 samples.

FANTOM5 promoters (47 alternative TSS)

Promoter ID	TPM avg	Samples expressed
43013	19.3228	1706
43030	10.2685	1328
43057	4.3599	526
43081	4.1642	1167
43001	3.6877	1303
43091	3.4126	1111
43003	3.2573	1146
43002	2.7687	1003
43031	2.5556	1014
43006	1.8775	523

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	99.86	gold quality
oviduct epithelium	UBERON:0004804	99.54	gold quality
cardia of stomach	UBERON:0001162	99.07	gold quality
saphenous vein	UBERON:0007318	99.02	gold quality
epithelial cell of pancreas	CL:0000083	98.98	gold quality
pylorus	UBERON:0001166	98.94	gold quality
ileal mucosa	UBERON:0000331	98.82	gold quality
pericardium	UBERON:0002407	98.76	gold quality
urethra	UBERON:0000057	98.67	gold quality
buccal mucosa cell	CL:0002336	98.60	gold quality
epithelium of mammary gland	UBERON:0003244	98.60	gold quality
mammary duct	UBERON:0001765	98.59	gold quality
vena cava	UBERON:0004087	98.58	gold quality
endothelial cell	CL:0000115	98.55	gold quality
parotid gland	UBERON:0001831	98.55	gold quality
calcaneal tendon	UBERON:0003701	98.45	gold quality
layer of synovial tissue	UBERON:0007616	98.36	gold quality
superior surface of tongue	UBERON:0007371	98.34	gold quality
colonic epithelium	UBERON:0000397	98.24	gold quality
trachea	UBERON:0003126	98.22	gold quality
lower lobe of lung	UBERON:0008949	98.18	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.06	gold quality
superficial temporal artery	UBERON:0001614	98.03	gold quality
synovial joint	UBERON:0002217	98.02	gold quality
visceral pleura	UBERON:0002401	97.92	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.70	gold quality
bronchus	UBERON:0002185	97.54	gold quality
trigeminal ganglion	UBERON:0001675	97.50	gold quality
bronchial epithelial cell	CL:0002328	97.49	gold quality
penis	UBERON:0000989	97.36	gold quality

Single-cell (SCXA)

Detected in 20 experiment(s), a significant marker in 13.

Experiment	Marker?	Max mean expression
E-MTAB-8894	yes	1617.22
E-HCAD-5	yes	1151.51
E-HCAD-4	yes	115.46
E-CURD-122	yes	58.15
E-GEOD-135922	yes	40.86
E-CURD-119	yes	36.71
E-CURD-114	yes	18.90
E-HCAD-10	yes	17.49
E-MTAB-6701	yes	13.22
E-MTAB-8410	yes	9.77
E-MTAB-9801	yes	6.62
E-CURD-46	yes	5.67
E-MTAB-11011	no	1872.99
E-MTAB-9221	no	841.42
E-MTAB-8207	no	539.75

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

38 targets.

Target	Regulation
AR
CD22	Repression
CDKN1A	Unknown
CDKN1C	Activation
CEL
CSF1R	Repression
ESR1
FGF16
FGF17
FGF18
FGF20
FGF3
FOXP1
GDF3
GJA1
GZMB
HIP1R	Unknown
IFNG
IL2	Unknown
IL6	Repression
IL7R
KLK3	Repression
LHX3
MYC	Activation
MYH6
MYH7
NKX2-5	Unknown
PITX3	Activation
RAG1	Unknown
RAG2	Activation

JASPAR motifs

Motif	Name	Family
MA0481.1	FOXP1	FOX
MA0481.2	FOXP1	FOX
MA0481.3	FOXP1	FOX
MA0481.4	FOXP1	FOX

JASPAR matrix evidence (PMIDs): PMID:21924763

Upstream regulators (CollecTRI, top): AR, ESR1, FOXP1, FOXP4, NR1I2, NR4A1

miRNA regulators (miRDB)

138 targeting FOXP1, 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-8485	100.00	77.57	4731
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-19A-3P	99.98	75.33	2762

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

• The FOXP1 winged helix transcription factor is a novel candidate tumor suppressor gene on chromosome 3p. (PMID:11751404)
• Foxp1, although broadly expressed, is further regulated by tissue-specific alternative splicing of its functionally important sequence domains (PMID:12692134)
• complex regulatory mechanism underlying Foxp1, Foxp2, and Foxp4 activity, demonstrating that Foxp1, Foxp2, and Foxp4 are the first Fox proteins reported whose activity is regulated by homo- and heterodimerization (PMID:14701752)
• FOXP1 and FOXP2 expression patterns in human fetal brain are strikingly similar to those in the songbird, including localization to subcortical structures that function in sensorimotor integration and the control of skilled, coordinated movement (PMID:15056695)
• FOXP1 is a potential ER coregulator in human breast carcinoma and may also independently regulate additional important pathways that control the progression of breast cancer (PMID:15161711)
• Integrin engagement regulates monocyte differentiation through FOXP1. (PMID:15286807)
• This study identifies FOXP1 as a new translocation partner of IGH in a site-dependent subset of MALT lymphomas. (PMID:15703784)
• Results suggest that FOXP1 expression may be important in diffuse large B-cell lymphoma (DLBCL) pathogenesis. (PMID:15709173)
• The heterogeneity of FOXP1 expression in germinal centre-derived lymphomas, may have more to do with the transforming events underlying these distinct types of lymphoma than with their common origin. (PMID:16200457)
• Tumors with exclusively cytoplasmic expression of FOXP1 were linked with deep myometrial invasion. (PMID:16258506)
• FOXP1 expression is an independent prognostic factor in MALT lymphomas. A subgroup of nongerminal center DLBCLs (Diffuse Large B-Cell Lymphomas, those marked by FOXP1 expression and trisomy 3 and 18) might represent a large-cell variant of MALT lymphomas. (PMID:16636337)
• rearrangement of FOXP1 is detected in a subset of large B-cell lymphomas with extranodal presentation (PMID:16673020)
• these data implicate specific members of the FOX family of TFs (FOXC1, C2, P1, P4, and O1A) not previously suggested in heart failure pathogenesis. (PMID:16952980)
• Our results suggest that MALT1-specific translocations and FOXP1 rearrangements are not commonly involved in pathogenesis. (PMID:17199743)
• There may be a hormonal and hypoxia independent regulatory mechanism coordinating the expression of HIFs, the AR, and FOXP1 in prostate tumors. (PMID:17477366)
• Expression of the forkhead transcription factor FOXP1 is associated with that of estrogen receptor-beta in primary invasive breast carcinomas. (PMID:18026833)
• The expression of potentially oncogenic smaller FOXP1 isoforms may resolve the previously contradictory findings that FOXP1 represents a favorable prognostic marker in breast cancer and an adverse risk factor in B-cell lymphomas. (PMID:18077790)
• FOXP1 protein is present in human endometrium with evidence of cycle stage-dependent changes in expression. FOXP1 expression was found in endometriotic lesions but not in endometrial adenocarcinoma (PMID:18332236)
• Mechanisms other than translocation and copy number changes are responsible for FOXP1 overexpression in lymphoma. (PMID:18487996)
• FOXP1 directly interacts with androgen receptor (AR) and negatively regulates AR signaling ligand-dependently. (PMID:18640093)
• There was an association between FOXP1 and diffuse large B-cell lymphoma: significant relationship between BCL2 expression and FOXP1 genetic abnormalities. (PMID:18925695)
• expression of Bcl-2 and FOXP1 is associated with the non-germinal center phenotype, but only Bcl-2 expression continues to be of prognostic significance in DLBCL patients treated with immunochemotherapy (PMID:19141121)
• FOXP1 mutations have a role in developmental verbal dyspraxia (PMID:19352412)
• FOXP1 expression is correlated with morphic histology and may be a biomarker for assessment of malignant transformation. (PMID:19365123)
• present in patients with higher clinical stages of chronic lymphocytic leukemia (PMID:19417623)
• FOXP1 might play an important role in plasma cell neoplasm. (PMID:19432679)
• Atypical FOXP1 expression in malignant plasma cells that show several simultaneous translocations (PMID:19438754)
• The expression of CD10, Bcl-6, MUM1/IRF4, Bcl-2, and FOXP1 was determined immunohistochemically from 88 samples of diffuse large B-cell lymphoma patients treated uniformly with R-CHOP (PMID:19448593)
• Our results provide strong evidence that relative FOXP1 isoform abundance is associated with NFkappaB activity in follicular lymphoma, and could potentially be used as a marker for this gene signature (PMID:19487025)
• Results suggest that FOXP1 demonstrates different expression patterns in familial breast cancers than sporadic tumours, even in tumours showing similar phenotypes, and also suggest a different role of FOXP1 as a tumour suppressor in familial tumours. (PMID:19622517)
• truncated FOXP1 isoforms are preferentially overexpressed in primary central nervous system lymphomas (PMID:19680146)
• FOXP1 is not rearranged in Splenic marginal zone lymphoma (PMID:19760589)
• Studies illustrated tools for cut-off level determination with prognostic tumor-related biomarkers Bcl-2, Bcl-6, CD10, FOXP1, MUM1, and Cyclin E in DLBCL. (PMID:19925052)
• These results demonstrate a role of PKCdelta in alpha(M)beta(2)-mediated Foxp1 regulation in monocytes. (PMID:20190138)
• Data show a replicated association of generalized vitiligo with variants at 3p13 encompassing FOXP1. (PMID:20526340)
• FOXP1 overexpression was associated with poor disease-specific survival in all nodal diffuse large B-cell lymphomas. There was no correlation between FOXP1 gene aberrations and either FOXP1 protein expression or survival. (PMID:20579129)
• Found three heterozygous overlapping deletions solely affecting the FOXP1 gene. All three patients had moderate mental retardation and significant language and speech deficits. (PMID:20848658)
• both FOXP1 and FOXP2 are associated with language impairment, but decrease of the former has a more global impact on brain development than that of the latter. (PMID:20950788)
• FOXP1 might play a role in the pathogenesis of nodal diffuse large B-cell lymphoma . (PMID:21120478)
• Overexpression of FOXP1 is present in a considerable proportion of primary cutaneous large B cell lymphoma, leg type and might indicate an unfavourable prognosis. (PMID:21154235)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Foxp1	ENSMUSG00000030067
rattus_norvegicus	Foxp1	ENSRNOG00000009184

Paralogs (41): FOXP3 (ENSG00000049768), FOXC1 (ENSG00000054598), FOXJ2 (ENSG00000065970), FOXF1 (ENSG00000103241), FOXN1 (ENSG00000109101), FOXM1 (ENSG00000111206), FOXO3 (ENSG00000118689), FOXA2 (ENSG00000125798), FOXA1 (ENSG00000129514), FOXJ1 (ENSG00000129654), FOXK2 (ENSG00000141568), FOXO1 (ENSG00000150907), FOXH1 (ENSG00000160973), FOXQ1 (ENSG00000164379), FOXK1 (ENSG00000164916), FOXD4 (ENSG00000170122), FOXA3 (ENSG00000170608), FOXB1 (ENSG00000171956), FOXR1 (ENSG00000176302), FOXL1 (ENSG00000176678), FOXC2 (ENSG00000176692), FOXE1 (ENSG00000178919), FOXS1 (ENSG00000179772), FOXL2 (ENSG00000183770), FOXO4 (ENSG00000184481), FOXD4L1 (ENSG00000184492), FOXD4L4 (ENSG00000184659), FOXD2 (ENSG00000186564), FOXI2 (ENSG00000186766), FOXE3 (ENSG00000186790), FOXD3 (ENSG00000187140), FOXD4L3 (ENSG00000187559), FOXR2 (ENSG00000189299), FOXJ3 (ENSG00000198815), FOXO6 (ENSG00000204060), FOXB2 (ENSG00000204612), FOXD4L5 (ENSG00000204779), FOXI3 (ENSG00000214336), FOXL3 (ENSG00000248767), FOXD1 (ENSG00000251493)

Protein

Protein identifiers

Forkhead box protein P1 — Q9H334 (reviewed: Q9H334)

Alternative names: Mac-1-regulated forkhead

All UniProt accessions (25): Q9H334, A0A087X2G3, A0A0B4J2F3, A0A3B3IRL7, A0A3B3IRS5, A0A3B3IRW5, A0A3B3IRY1, A0A3B3IS87, A0A3B3ISA4, A0A3B3ISQ7, A0A3B3IST0, A0A3B3IST6, A0A3B3IT14, A0A3B3IT26, A0A3B3IT66, A0A3B3ITZ4, A0A3B3IU08, A0A3B3IU15, A0A3B3IUB6, C9IYY1, C9J0F0, C9J5T4, G5E965, H0Y882, Q548T7

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional repressor. Can act with CTBP1 to synergistically repress transcription but CTPBP1 is not essential. Plays an important role in the specification and differentiation of lung epithelium. Acts cooperatively with FOXP4 to regulate lung secretory epithelial cell fate and regeneration by restricting the goblet cell lineage program; the function may involve regulation of AGR2. Essential transcriptional regulator of B-cell development. Involved in regulation of cardiac muscle cell proliferation. Involved in the columnar organization of spinal motor neurons. Promotes the formation of the lateral motor neuron column (LMC) and the preganglionic motor column (PGC) and is required for respective appropriate motor axon projections. The segment-appropriate generation of spinal cord motor columns requires cooperation with other Hox proteins. Can regulate PITX3 promoter activity; may promote midbrain identity in embryonic stem cell-derived dopamine neurons by regulating PITX3. Negatively regulates the differentiation of T follicular helper cells T(FH)s. Involved in maintenance of hair follicle stem cell quiescence; the function probably involves regulation of FGF18. Represses transcription of various pro-apoptotic genes and cooperates with NF-kappa B-signaling in promoting B-cell expansion by inhibition of caspase-dependent apoptosis. Binds to CSF1R promoter elements and is involved in regulation of monocyte differentiation and macrophage functions; repression of CSF1R in monocytes seems to involve NCOR2 as corepressor. Involved in endothelial cell proliferation, tube formation and migration indicative for a role in angiogenesis; the role in neovascularization seems to implicate suppression of SEMA5B. Can negatively regulate androgen receptor signaling. Acts as a transcriptional activator of the FBXL7 promoter; this activity is regulated by AURKA. Involved in transcriptional regulation in embryonic stem cells (ESCs). Stimulates expression of transcription factors that are required for pluripotency and decreases expression of differentiation-associated genes. Has distinct DNA-binding specifities as compared to the canonical form and preferentially binds DNA with the sequence 5’-CGATACAA-3’ (or closely related sequences). Promotes ESC self-renewal and pluripotency.

Subunit / interactions. Forms homodimers and heterodimers with FOXP2 and FOXP4. Dimerization is required for DNA-binding. Self-associates. Interacts with CTBP1. Interacts with NCOR2 and AR. Interacts with FOXP2. Interacts with TBR1. Interacts with AURKA; this interaction facilitates the phosphorylation of FOXP1, which suppresses the expression of FBXL7. Interacts with ZMYM2.

Subcellular location. Nucleus.

Tissue specificity. Isoform 8 is specifically expressed in embryonic stem cells.

Disease relevance. A chromosomal aberration involving FOXP1 is found in acute lymphoblastic leukemia. Translocation t(9;3)(p13;p14.1) with PAX5. Intellectual developmental disorder with language impairment and with or without autistic features (IDDLA) [MIM:613670] A developmental disorder characterized by mild to moderate intellectual disability, language impairment, and autistic features in some patients. Patients show global delay, delayed walking, severely delayed speech development, and behavioral abnormalities, including irritability, hyperactivity, aggression, and stereotypical rigid behaviors. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The leucine zipper (ZIP) is required for dimerization and transcriptional repression.

Induction. By androgen in an isoform-specific manner; expression of isoform 4 is greatly induced.

Miscellaneous. Incomplete sequence. Incomplete sequence. May be due to competing acceptor splice site.

Isoforms (7)

UniProt ID	Names	Canonical?
Q9H334-1	1	yes
Q9H334-3	3
Q9H334-4	4
Q9H334-5	5
Q9H334-6	6
Q9H334-7	7
Q9H334-8	8, FOXP1-ES

RefSeq proteins (17): NP_001012523, NP_001231737, NP_001231739, NP_001231741, NP_001231742, NP_001231743, NP_001231744, NP_001231745, NP_001336266, NP_001336267, NP_001336269, NP_001336270, NP_001336271, NP_001336272, NP_001336273, NP_001357477, NP_116071 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001766	Fork_head_dom	Domain
IPR030456	TF_fork_head_CS_2	Conserved_site
IPR032354	FOXP-CC	Domain
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR047412	FH_FOXP1_P2	Domain
IPR050998	FOXP	Family

Pfam: PF00250, PF16159

UniProt features (55 total): sequence variant 13, compositionally biased region 7, splice variant 6, region of interest 5, helix 5, cross-link 4, sequence conflict 4, modified residue 3, strand 3, chain 1, domain 1, site 1, zinc finger region 1, DNA-binding region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2KIU	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H334-F1	59.27	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.

Catalytic / active sites (1): 59–60 (breakpoint for translocation to form pax5-foxp1)

Post-translational modifications (7): 83, 653, 658, 287, 372, 377, 442

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-452723	Transcriptional regulation of pluripotent stem cells

MSigDB gene sets: 0 (showing top):

GO Biological Process (36): negative regulation of B cell apoptotic process (GO:0002903), regulation of transcription by RNA polymerase II (GO:0006357), DNA damage response (GO:0006974), regulation of gene expression (GO:0010468), positive regulation of endothelial cell migration (GO:0010595), negative regulation of gene expression (GO:0010629), striatum development (GO:0021756), osteoclast differentiation (GO:0030316), response to lipopolysaccharide (GO:0032496), regulation of interleukin-1 beta production (GO:0032651), regulation of interleukin-12 production (GO:0032655), regulation of tumor necrosis factor production (GO:0032680), positive regulation of interleukin-21 production (GO:0032745), response to testosterone (GO:0033574), osteoclast development (GO:0036035), macrophage activation (GO:0042116), monocyte activation (GO:0042117), endothelial cell activation (GO:0042118), regulation of monocyte differentiation (GO:0045655), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of smooth muscle cell proliferation (GO:0048661), regulation of inflammatory response (GO:0050727), positive regulation of B cell receptor signaling pathway (GO:0050861), negative regulation of androgen receptor signaling pathway (GO:0060766), negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052), T follicular helper cell differentiation (GO:0061470), cellular response to tumor necrosis factor (GO:0071356), regulation of defense response to bacterium (GO:1900424), regulation of macrophage colony-stimulating factor production (GO:1901256), positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300), regulation of endothelial tube morphogenesis (GO:1901509), regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000341), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355), forebrain development (GO:0030900), animal organ development (GO:0048513)

GO Molecular Function (13): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), core promoter sequence-specific DNA binding (GO:0001046), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), identical protein binding (GO:0042802), nuclear androgen receptor binding (GO:0050681), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	3
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
gene expression	2
response to lipid	2
myeloid leukocyte activation	2
transcription cis-regulatory region binding	2
cellular anatomical structure	2
B cell apoptotic process	1
regulation of B cell apoptotic process	1
negative regulation of lymphocyte apoptotic process	1
transcription by RNA polymerase II	1
cellular response to stress	1
regulation of macromolecule biosynthetic process	1
regulation of endothelial cell migration	1
positive regulation of cell migration	1
endothelial cell migration	1
regulation of gene expression	1
negative regulation of macromolecule biosynthetic process	1
subpallium development	1
anatomical structure development	1
myeloid leukocyte differentiation	1
response to molecule of bacterial origin	1
response to oxygen-containing compound	1
interleukin-1 beta production	1
regulation of interleukin-1 production	1
regulation of cytokine production	1
interleukin-12 production	1
tumor necrosis factor production	1
regulation of tumor necrosis factor superfamily cytokine production	1
positive regulation of cytokine production	1
interleukin-21 production	1
regulation of interleukin-21 production	1
response to ketone	1
osteoclast differentiation	1
myeloid cell development	1
bone cell development	1
cell activation	1
regulation of myeloid leukocyte differentiation	1
monocyte differentiation	1
DNA-templated transcription	1

Protein interactions and networks

STRING

2496 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FOXP1	IGHV4-38-2	P0DP08	794
FOXP1	IL1F10	Q8WWZ1	762
FOXP1	NCOR2	Q9Y618	738
FOXP1	TBR1	Q16650	707
FOXP1	KPNA7	A9QM74	695
FOXP1	MYC	P01106	659
FOXP1	MME	P08473	656
FOXP1	FOXP4	Q8IVH2	655
FOXP1	CNTNAP2	Q9UHC6	646
FOXP1	SATB2	Q9UPW6	637
FOXP1	MTA1	Q13330	625
FOXP1	BCL6	P41182	624
FOXP1	SERPINA9	Q86WD7	620
FOXP1	EBF1	Q9UH73	619
FOXP1	GATA3	P23771	609

IntAct

112 interactions, top by confidence:

A	B	Type	Score
MTOR	RICTOR	psi-mi:“MI:0914”(association)	0.970
FOXP1	FOXP2	psi-mi:“MI:0914”(association)	0.910
FOXP2	FOXP1	psi-mi:“MI:2364”(proximity)	0.910
FOXP2	FOXP1	psi-mi:“MI:0403”(colocalization)	0.910
FOXP2	FOXP1	psi-mi:“MI:0915”(physical association)	0.910
FOXP1	FOXP2	psi-mi:“MI:0403”(colocalization)	0.910
FOXP1	FOXP2	psi-mi:“MI:0915”(physical association)	0.910
FOXP4	FOXP2	psi-mi:“MI:0914”(association)	0.770
FOXP2	FOXP4	psi-mi:“MI:0914”(association)	0.770
FOXP2	FOXP2	psi-mi:“MI:0914”(association)	0.740
FOXP1	FOXP1	psi-mi:“MI:2364”(proximity)	0.710
FOXP1	FOXP1	psi-mi:“MI:0403”(colocalization)	0.710
FOXP1	FOXP1	psi-mi:“MI:0915”(physical association)	0.710
NFIC	NFIB	psi-mi:“MI:2364”(proximity)	0.690
FOXP1	FOXP4	psi-mi:“MI:0915”(physical association)	0.600
FOXP1	FOXP4	psi-mi:“MI:0403”(colocalization)	0.600
	NFATC2	psi-mi:“MI:0914”(association)	0.590
FOXP3	FOXP2	psi-mi:“MI:0914”(association)	0.530
FHL2	CNOT1	psi-mi:“MI:0914”(association)	0.530
LRRK1	FOXP1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (331): FOXP1 (Affinity Capture-MS), FOXP1 (Affinity Capture-RNA), FOXP2 (Affinity Capture-MS), FOXP4 (Affinity Capture-MS), RCC1 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), QSER1 (Affinity Capture-MS), SATB1 (Affinity Capture-MS), SATB2 (Affinity Capture-MS), CTBP2 (Affinity Capture-MS), MYH10 (Affinity Capture-MS), LIG3 (Affinity Capture-MS), C10orf2 (Affinity Capture-MS), CUX1 (Affinity Capture-MS), VRK3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JTZ2, A2BEA6, A4IFD2, B1H349, B3DM43, B3DM47, F1M8W4, O15409, O75030, P0CF24, P23899, P27889, P35680, P35710, P35711, P35712, P40645, P40647, P58463, P70062, P70063, P70064, Q23045, Q2LE08, Q4VYR7, Q4VYS1, Q58NQ4, Q5QL03, Q5RCU4, Q5RER5, Q5W1J5, Q6GL68, Q800Q5, Q86MD3, Q8HZ00, Q8MJ97, Q8MJ98, Q8MJ99, Q8MJA0, Q8STF6

Diamond homologs: A0A2Z4LIS9, A0A8V0YY16, A3RK74, A3RK75, A4IFD2, A4L7N3, A8MTJ6, A8MYZ6, A8XJN7, B3LYS5, B3P0K6, B4G4S8, B4HF64, B4JSC2, B4KBF6, B4MB78, B4NFR1, B4PTD3, B5RHS5, E1BPQ1, G3V7R4, O00409, O16850, O43524, O88470, P25364, P32031, P32315, P33205, P33206, P55316, P56260, P58012, P58462, P98177, Q00939, Q02361, Q12778, Q12948, Q12951

SIGNOR signaling

6 interactions.

A	Effect	B	Mechanism
FOXP1	“down-regulates quantity by repression”	HIP1R	“transcriptional regulation”
FOXP1	“down-regulates quantity by repression”	KLK3	“transcriptional regulation”
FOXP1	“down-regulates quantity by repression”	CSF1R	“transcriptional regulation”
miRNA‑22‑3p	“down-regulates quantity by destabilization”	FOXP1	“post transcriptional regulation”
FOXP1	“up-regulates quantity by expression”	PITX3	“transcriptional regulation”
FOXP1	“down-regulates quantity by repression”	SEMA5B	“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 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
Deactivation of the beta-catenin transactivating complex	7	25.5×	2e-06
TCF dependent signaling in response to WNT	9	16.6×	2e-06
Signaling by WNT	8	14.0×	2e-05
PIP3 activates AKT signaling	6	6.3×	9e-03

GO biological processes:

GO term	Partners	Fold	FDR
neuron fate specification	5	39.9×	2e-05
branching involved in ureteric bud morphogenesis	6	25.0×	2e-05
positive regulation of miRNA transcription	7	23.1×	4e-06
chondrocyte differentiation	5	17.1×	6e-04
cartilage development	5	14.3×	1e-03
somatic stem cell population maintenance	5	14.1×	1e-03
transcription by RNA polymerase II	16	12.8×	2e-11
anatomical structure morphogenesis	7	11.1×	2e-04

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 2 cancer types — BRCA, PRAD.

Clinical variants and AI predictions

ClinVar

1116 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	132
Likely pathogenic	67
Uncertain significance	369
Likely benign	377
Benign	63

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1065605	NM_001349338.3(FOXP1):c.1426C>T (p.Gln476Ter)	Pathogenic
1164044	NM_001349338.3(FOXP1):c.1553G>A (p.Ser518Asn)	Pathogenic
1184108	NM_001349338.3(FOXP1):c.1722G>A (p.Gln574=)	Pathogenic
1298925	NM_001349338.3(FOXP1):c.214C>T (p.Gln72Ter)	Pathogenic
1452906	NM_001349338.3(FOXP1):c.1087C>T (p.Gln363Ter)	Pathogenic
1453357	NM_001349338.3(FOXP1):c.1264del (p.Ser422fs)	Pathogenic
1457940	NM_001349338.3(FOXP1):c.1031_1032insT (p.Gln344fs)	Pathogenic
1527024	GRCh37/hg19 3p13(chr3:71008556-71049017)	Pathogenic
1527025	GRCh37/hg19 3p13(chr3:71251088-71312384)	Pathogenic
156540	NC_000003.12:g.70992485_71180270del	Pathogenic
1679344	NM_001349338.3(FOXP1):c.488del (p.His163fs)	Pathogenic
1679348	NM_001349338.3(FOXP1):c.825del (p.Ser276fs)	Pathogenic
1685827	NM_001349338.3(FOXP1):c.2018del (p.Asn673fs)	Pathogenic
1685828	NM_001349338.3(FOXP1):c.975-2A>G	Pathogenic
1698739	NM_001349338.3(FOXP1):c.738del (p.Asn247fs)	Pathogenic
1699444	NM_001349338.3(FOXP1):c.1653_1669del (p.Asn552fs)	Pathogenic
1701967	NM_001349338.3(FOXP1):c.494del (p.Gly165fs)	Pathogenic
1711578	NM_001349338.3(FOXP1):c.508G>T (p.Glu170Ter)	Pathogenic
1802625	NM_001349338.3(FOXP1):c.1569_1570insA (p.Val524fs)	Pathogenic
1803026	NM_001349338.3(FOXP1):c.573dup (p.Gln192fs)	Pathogenic
1803027	NM_001349338.3(FOXP1):c.580C>T (p.Gln194Ter)	Pathogenic
1805541	NM_001349338.3(FOXP1):c.1147-1_1161dup	Pathogenic
1805564	NM_001349338.3(FOXP1):c.1241del (p.Leu414fs)	Pathogenic
1806120	NM_001349338.3(FOXP1):c.482_483dup (p.Gln162fs)	Pathogenic
18427	NC_000003.10:g.(71109689_?)_(?_71508061)del	Pathogenic
18428	NM_001349338.3(FOXP1):c.1573C>T (p.Arg525Ter)	Pathogenic
194566	NM_001349338.3(FOXP1):c.1317C>A (p.Tyr439Ter)	Pathogenic
194567	NM_001349338.3(FOXP1):c.1240dup (p.Leu414fs)	Pathogenic
194896	NM_001349338.3(FOXP1):c.1624C>T (p.Gln542Ter)	Pathogenic
1992885	NM_001349338.3(FOXP1):c.909T>G (p.Tyr303Ter)	Pathogenic

SpliceAI

8587 predictions. Top by Δscore:

Variant	Effect	Δscore
3:70959203:T:TA	donor_gain	1.0000
3:70959389:TGC:T	acceptor_gain	1.0000
3:70959390:GCC:G	acceptor_loss	1.0000
3:70959392:C:CC	acceptor_gain	1.0000
3:70959392:CTGGA:C	acceptor_loss	1.0000
3:70970801:GGTTA:G	acceptor_gain	1.0000
3:70970803:TTA:T	acceptor_gain	1.0000
3:70970804:TA:T	acceptor_gain	1.0000
3:70970806:C:CC	acceptor_gain	1.0000
3:70970808:G:C	acceptor_gain	1.0000
3:70970808:G:GC	acceptor_gain	1.0000
3:70972005:TCTTA:T	donor_loss	1.0000
3:70972006:CTTA:C	donor_loss	1.0000
3:70972007:TTA:T	donor_loss	1.0000
3:70972008:TA:T	donor_loss	1.0000
3:70972009:A:AC	donor_gain	1.0000
3:70972009:ACTG:A	donor_loss	1.0000
3:70972010:C:A	donor_loss	1.0000
3:70972010:C:CA	donor_gain	1.0000
3:70972010:CT:C	donor_gain	1.0000
3:70972010:CTGTG:C	donor_gain	1.0000
3:70972554:CCCA:C	donor_gain	1.0000
3:70972557:A:AC	donor_gain	1.0000
3:70972558:C:CC	donor_gain	1.0000
3:70972558:CTGAT:C	donor_gain	1.0000
3:70972686:G:GC	acceptor_gain	1.0000
3:70976935:GCTTA:G	donor_loss	1.0000
3:70976936:CTTAC:C	donor_loss	1.0000
3:70976937:TTA:T	donor_loss	1.0000
3:70976938:TACCT:T	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000000694 (3:71385964 C>T), RS1000002497 (3:70959113 A>G,T), RS1000017142 (3:71446794 T>C), RS1000026306 (3:71487642 T>C), RS1000027272 (3:71232842 G>A,C), RS1000042085 (3:71508164 A>AG), RS1000042325 (3:71566424 T>C), RS1000043212 (3:71573435 C>A), RS1000043871 (3:71179577 A>G), RS1000051094 (3:71519280 T>C,G), RS1000051236 (3:71311013 C>A), RS1000055531 (3:70985726 C>T), RS1000059880 (3:71232695 T>G), RS1000063210 (3:71067548 C>T), RS1000065689 (3:71182541 T>C)

Disease associations

OMIM: gene MIM:605515 | disease phenotypes: MIM:613670, MIM:108800, MIM:213000, MIM:209850, MIM:178370, MIM:241550, MIM:306955, MIM:606215

GenCC curated gene-disease

Disease	Classification	Inheritance
intellectual disability-severe speech delay-mild dysmorphism syndrome	Definitive	Autosomal dominant
congenital heart disease	Disputed Evidence	Autosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
intellectual disability-severe speech delay-mild dysmorphism syndrome	Definitive	AD
congenital heart disease	Disputed	AD

Mondo (16): intellectual disability-severe speech delay-mild dysmorphism syndrome (MONDO:0013352), autism spectrum disorder (MONDO:0005258), intellectual disability (MONDO:0001071), atrial septal defect 1 (MONDO:0007172), disorder of sexual differentiation (MONDO:0002145), neurodevelopmental disorder (MONDO:0700092), congenital heart disease (MONDO:0005453), isolated cerebellar hypoplasia/agenesis (MONDO:0008939), strabismus (MONDO:0003432), autism (MONDO:0005260), pulmonary atresia with ventricular septal defect (MONDO:0008343), hypoplastic left heart syndrome 1 (MONDO:0009433), mitral atresia disorder (MONDO:0015249), visceral heterotaxy (MONDO:0018677), aortic valve atresia (MONDO:0019808)

Orphanet (15): FOXP1 Syndrome (Orphanet:391372), Interatrial communication (Orphanet:1478), Difference of sex development (Orphanet:90771), Isolated cerebellar agenesis (Orphanet:1398), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246), Mitral atresia (Orphanet:1205), Pulmonary atresia with ventricular septal defect (Orphanet:1207), Hypoplastic left heart syndrome (Orphanet:2248), Visceral heterotaxy (Orphanet:450), Congenital aortic valve atresia (Orphanet:95448), Atrioventricular septal defect (Orphanet:98722), Rare genetic intellectual disability (Orphanet:183757), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658), Situs ambiguus (Orphanet:157769)

HPO phenotypes

98 total (30 of 98 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000077	Abnormality of the kidney
HP:0000119	Abnormality of the genitourinary system
HP:0000194	Open mouth
HP:0000256	Macrocephaly
HP:0000272	Malar flattening
HP:0000278	Retrognathia
HP:0000303	Mandibular prognathia
HP:0000316	Hypertelorism
HP:0000403	Recurrent otitis media
HP:0000455	Broad nasal tip
HP:0000478	Abnormality of the eye
HP:0000486	Strabismus
HP:0000494	Downslanted palpebral fissures
HP:0000505	Visual impairment
HP:0000508	Ptosis
HP:0000539	Abnormality of refraction
HP:0000581	Blepharophimosis
HP:0000598	Abnormality of the ear
HP:0000614	Abnormal nasolacrimal system morphology
HP:0000639	Nystagmus
HP:0000708	Atypical behavior
HP:0000718	Aggressive behavior
HP:0000722	Compulsive behaviors
HP:0000729	Autistic behavior
HP:0000732	Inflexible adherence to routines
HP:0000733	Motor stereotypy
HP:0000736	Short attention span
HP:0000739	Anxiety
HP:0000750	Delayed speech and language development

GWAS associations

112 associations (top):

Study	Trait	p-value
GCST000281_14	Attention deficit hyperactivity disorder	6.000000e-06
GCST001521_18	Subcutaneous adipose tissue	2.000000e-06
GCST002168_9	Intraocular pressure	5.000000e-06
GCST002230_1	Barrett’s esophagus	2.000000e-06
GCST002231_1	Digestive system disease (Barrett’s esophagus and esophageal adenocarcinoma combined)	5.000000e-09
GCST002232_1	Esophageal adenocarcinoma	6.000000e-07
GCST003327_7	Squamous cell carcinoma	1.000000e-08
GCST003726_20	Basal cell carcinoma	2.000000e-17
GCST003740_6	Barrett’s esophagus or Esophageal adenocarcinoma	2.000000e-09
GCST003814_16	Selective IgA deficiency	3.000000e-06
GCST003999_1	Nose size	8.000000e-26
GCST004030_13	Primary sclerosing cholangitis	3.000000e-15
GCST004030_18	Primary sclerosing cholangitis	2.000000e-08
GCST004131_5	Inflammatory bowel disease	3.000000e-09
GCST004132_2	Crohn’s disease	7.000000e-06
GCST004521_34	Autism spectrum disorder or schizophrenia	1.000000e-08
GCST004601_45	Red blood cell count	7.000000e-14
GCST004602_130	Mean corpuscular volume	6.000000e-13
GCST004627_98	Lymphocyte count	4.000000e-20
GCST004630_118	Mean corpuscular hemoglobin	6.000000e-12
GCST004632_143	Lymphocyte percentage of white cells	2.000000e-16
GCST004632_144	Lymphocyte percentage of white cells	4.000000e-11
GCST004633_115	Neutrophil percentage of white cells	8.000000e-11
GCST004639_41	Prudent dietary pattern	9.000000e-06
GCST004764_3	LDL cholesterol change in response to fenofibrate in statin-treated type 2 diabetes	9.000000e-07
GCST004785_20	Vitiligo	8.000000e-19
GCST004988_636	Breast cancer	5.000000e-08
GCST005141_35	Cognitive ability (MTAG)	4.000000e-09
GCST005316_134	Intelligence (MTAG)	2.000000e-10
GCST005391_1	Tooth agenesis (maxillary lateral incisors)	1.000000e-11

EFO canonical traits (37, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0004305	erythrocyte count
EFO:0004587	lymphocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes
EFO:0008111	diet measurement
EFO:0007804	LDL cholesterol change measurement
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment
EFO:0006941	grip strength measurement
EFO:0009260	non-melanoma skin carcinoma
EFO:0006953	family history of lung cancer
EFO:0005763	pulse pressure measurement
EFO:0006335	systolic blood pressure
EFO:0008579	risk-taking behaviour
EFO:0004312	vital capacity
EFO:0004314	forced expiratory volume
EFO:0008328	chronotype measurement
EFO:0010176	keratinocyte carcinoma
EFO:0010476	dimethylglycine measurement
EFO:0005213	central corneal thickness
EFO:0009695	household income
EFO:0007979	childhood trauma measurement
EFO:1001927	cutaneous squamous cell carcinoma
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004462	PR interval
EFO:0007874	gut microbiome measurement
EFO:0004346	neuroimaging measurement
EFO:0004327	electrocardiography

MeSH disease descriptors (8)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500
D012734	Disorders of Sex Development	C12.050.351.875.253; C12.200.706.316; C12.800.316; C16.131.939.316; C19.391.119
D006330	Heart Defects, Congenital	C14.240.400; C14.280.400; C16.131.240.400
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065886	Neurodevelopmental Disorders	F03.625
D013285	Strabismus	C10.292.562.887; C11.590.810
C562568	Cerebellar Hypoplasia (supp.)
C562833	Pulmonary Atresia With Ventricular Septal Defect (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	5
bisphenol A	increases methylation, decreases expression, increases expression, affects methylation, affects cotreatment	4
Benzo(a)pyrene	decreases expression, increases methylation, affects methylation	3
potassium chromate(VI)	affects cotreatment, decreases expression	2
Air Pollutants	affects cotreatment, decreases expression, increases abundance	2
Arsenic	affects methylation, increases methylation	2
Dexamethasone	affects cotreatment, increases expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Aflatoxin B1	increases methylation	2
Particulate Matter	decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
AKT activator SC79	increases secretion, decreases reaction, increases expression	1
napabucasin	decreases expression	1
TAK-243	decreases sumoylation	1
TL8-506	affects cotreatment, increases expression	1
methylmercuric chloride	increases expression	1
alpha-pinene	decreases expression, increases abundance, affects cotreatment	1
pirinixic acid	affects binding, decreases expression, increases activity	1
4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
chromium hexavalent ion	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1

Cellosaurus cell lines

6 cell lines: 3 embryonic stem cell, 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A2D0	SEES3-1V human FOXP1, clone1	Embryonic stem cell	Male
CVCL_A2D1	SEES3-1V human FOXP1, clone2	Embryonic stem cell	Male
CVCL_A2D2	SEES3-1V human FOXP1, clone3	Embryonic stem cell	Male
CVCL_B8GI	Abcam HCT 116 FOXP1 KO	Cancer cell line	Male
CVCL_B8W4	Abcam MCF-7 FOXP1 KO	Cancer cell line	Female
CVCL_B9IS	Abcam A-549 FOXP1 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00668824	PHASE4	UNKNOWN	Improved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705	PHASE4	COMPLETED	Nitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982	PHASE4	COMPLETED	Pre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679	PHASE4	WITHDRAWN	Tranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811	PHASE4	UNKNOWN	Ulinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700	PHASE4	COMPLETED	Fibrinogen Concentrate vs Cryoprecipitate
NCT03408340	PHASE4	TERMINATED	Paravertebral Nerve Blocks in Neonates
NCT03630796	PHASE4	UNKNOWN	Effect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703	PHASE4	COMPLETED	Stress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761	PHASE4	UNKNOWN	Thiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389	PHASE4	RECRUITING	Sodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154	PHASE4	NOT_YET_RECRUITING	Perioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT00000470	PHASE3	COMPLETED	Infant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494	PHASE3	COMPLETED	Management of Patent Ductus in Premature Infants
NCT01134302	PHASE3	UNKNOWN	Hybrid Versus Norwood Management Strategies in Infants Undergoing Single Ventricle Palliation
NCT01607983	PHASE3	WITHDRAWN	Effects of Pulmonary Vasodilation Upon VA Coupling in Fontan Patients
NCT01662011	PHASE3	UNKNOWN	Application of Neurally Adjusted Ventilatory Assist to Children After Congenital Cardiac Surgery
NCT02320669	PHASE3	COMPLETED	Phase 3 Triiodothyronine Supplementation for Infants After Cardiopulmonary Bypass
NCT02615262	PHASE3	COMPLETED	Intraoperative Dexamethasone in Pediatric Cardiac Surgery