INTS13

Summary

INTS13 (integrator complex subunit 13, HGNC:20174) is a protein-coding gene on chromosome 12p11.23, encoding Integrator complex subunit 13 (Q9NVM9). Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. It is a selective cancer dependency (DepMap: 29.7% of cell lines).

Involved in regulation of mitotic cell cycle. Acts upstream of or within centrosome localization; mitotic spindle organization; and protein localization to nuclear envelope. Located in cytoplasm and nuclear body. Part of integrator complex. Is active in nucleus.

Source: NCBI Gene 55726 — RefSeq curated summary.

At a glance

• Gene–disease (curated): orofaciodigital syndrome (Strong, GenCC)
• GWAS associations: 4
• Clinical variants (ClinVar): 74 total
• Cancer dependency (DepMap): dependent in 29.7% of screened cell lines
• MANE Select transcript: NM_018164

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20174
Approved symbol	INTS13
Name	integrator complex subunit 13
Location	12p11.23
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10637, NET48, Mat89Bb, SPATA30
Ensembl gene	ENSG00000064102
Ensembl biotype	protein_coding
OMIM	615079
Entrez	55726

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 25 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000261191, ENST00000536232, ENST00000537336, ENST00000538016, ENST00000538155, ENST00000538727, ENST00000538748, ENST00000542392, ENST00000544548, ENST00000892606, ENST00000892607, ENST00000892608, ENST00000892609, ENST00000892610, ENST00000892611, ENST00000892612, ENST00000892613, ENST00000892614, ENST00000892615, ENST00000892616, ENST00000892617, ENST00000892618, ENST00000892619, ENST00000912525, ENST00000946630, ENST00000946631, ENST00000946632, ENST00000946633

RefSeq mRNA: 1 — MANE Select: NM_018164 NM_018164

CCDS: CCDS8708

Canonical transcript exons

ENST00000261191 — 17 exons

Exon	Start	End
ENSE00000835898	26906302	26906437
ENSE00000835901	26911178	26911317
ENSE00001249321	26913457	26913687
ENSE00001346944	26937796	26937981
ENSE00001593772	26917352	26917441
ENSE00001626064	26936579	26936814
ENSE00001631630	26934556	26934630
ENSE00001646446	26922616	26922700
ENSE00001683532	26924355	26924483
ENSE00001701826	26928205	26928285
ENSE00001710128	26914408	26914578
ENSE00001731513	26917644	26917733
ENSE00001756219	26916002	26916180
ENSE00001785777	26913974	26914128
ENSE00002203749	26905181	26905536
ENSE00003527724	26928703	26928905
ENSE00003785496	26925761	26925851

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 93.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1206 / max 199.4382, expressed in 1791 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
130241	11.6889	1755
130242	2.1114	1323
130240	1.3203	886

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
esophagus squamous epithelium	UBERON:0006920	93.50	gold quality
secondary oocyte	CL:0000655	93.45	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	93.39	gold quality
epithelium of nasopharynx	UBERON:0001951	93.30	gold quality
nasopharynx	UBERON:0001728	93.28	gold quality
spinal cord	UBERON:0002240	93.05	gold quality
tibia	UBERON:0000979	92.92	gold quality
biceps brachii	UBERON:0001507	92.15	gold quality
germinal epithelium of ovary	UBERON:0001304	92.04	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	91.95	gold quality
gingival epithelium	UBERON:0001949	91.88	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.73	gold quality
gingiva	UBERON:0001828	91.61	gold quality
epithelium of esophagus	UBERON:0001976	91.19	gold quality
pigmented layer of retina	UBERON:0001782	91.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.02	gold quality
corpus callosum	UBERON:0002336	90.79	gold quality
eye	UBERON:0000970	90.74	gold quality
palpebral conjunctiva	UBERON:0001812	90.62	gold quality
oocyte	CL:0000023	90.60	gold quality
heart right ventricle	UBERON:0002080	90.52	gold quality
oral cavity	UBERON:0000167	90.32	gold quality
squamous epithelium	UBERON:0006914	90.22	gold quality
left adrenal gland	UBERON:0001234	90.14	gold quality
right adrenal gland	UBERON:0001233	90.10	gold quality
right adrenal gland cortex	UBERON:0035827	90.10	gold quality
parietal pleura	UBERON:0002400	90.05	gold quality
left adrenal gland cortex	UBERON:0035825	89.96	gold quality
adrenal cortex	UBERON:0001235	89.72	gold quality
upper leg skin	UBERON:0004262	89.47	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.52
E-GEOD-99795	no	166.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

39 targeting INTS13, 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-4673	100.00	66.64	1490
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-372-5P	99.41	69.11	2299
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-525-5P	99.35	66.85	1615

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 29.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• Data suggest that ASUN promotes perinuclear enrichment of dynein at G2/M that facilitates BICD2- and CENP-F-mediated anchoring of dynein to nuclear pore complexes. (PMID:23097494)
• ASUN is identified as a functional component of Integrator (INT), a multisubunit complex required for 3’-end processing of small nuclear RNAs. (PMID:23904267)
• INTS10-INTS13-INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module. (PMID:32647223)
• INTS13 variants causing a recessive developmental ciliopathy disrupt assembly of the Integrator complex. (PMID:36229431)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ints13	ENSDARG00000011764
mus_musculus	Ints13	ENSMUSG00000040250
rattus_norvegicus	Ints13	ENSRNOG00000001808
drosophila_melanogaster	asun	FBGN0020407
caenorhabditis_elegans		WBGENE00019822

Protein

Protein identifiers

Integrator complex subunit 13 — Q9NVM9 (reviewed: Q9NVM9)

Alternative names: Cell cycle regulator Mat89Bb homolog, Germ cell tumor 1, Protein asunder homolog, Sarcoma antigen NY-SAR-95

All UniProt accessions (6): Q9NVM9, F5H457, F5H5W1, F8VRX9, H0YH12, H0YIA9

UniProt curated annotations — full annotation on UniProt →

Function. Component of the integrator complex, a multiprotein complex that terminates RNA polymerase II (Pol II) transcription in the promoter-proximal region of genes. The integrator complex provides a quality checkpoint during transcription elongation by driving premature transcription termination of transcripts that are unfavorably configured for transcriptional elongation: the complex terminates transcription by (1) catalyzing dephosphorylation of the C-terminal domain (CTD) of Pol II subunit POLR2A/RPB1 and SUPT5H/SPT5, (2) degrading the exiting nascent RNA transcript via endonuclease activity and (3) promoting the release of Pol II from bound DNA. The integrator complex is also involved in terminating the synthesis of non-coding Pol II transcripts, such as enhancer RNAs (eRNAs), small nuclear RNAs (snRNAs), telomerase RNAs and long non-coding RNAs (lncRNAs). Within the integrator complex, INTS13 is part of the integrator tail module and acts as a platform for the recruitment of transcription factors at promoters. At prophase, mediates recruitment of cytoplasmic dynein to the nuclear envelope, a step important for proper centrosome-nucleus coupling. At G2/M phase, may be required for proper spindle formation and execution of cytokinesis.

Subunit / interactions. Component of the Integrator complex, composed of core subunits INTS1, INTS2, INTS3, INTS4, INTS5, INTS6, INTS7, INTS8, INTS9/RC74, INTS10, INTS11/CPSF3L, INTS12, INTS13, INTS14 and INTS15. The core complex associates with protein phosphatase 2A subunits PPP2CA and PPP2R1A, to form the Integrator-PP2A (INTAC) complex. INTS13 is part of the tail subcomplex, composed of INTS10, INTS13, INTS14 and INTS15. Interacts with transcription factors ZNF609 and ZNF655. Interacts with PAFAH1B1; this interaction may be required for proper recruitment of dynein complexes to the nuclear envelope at prophase.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Widely expressed. Tends to be up-regulated in seminomas compared to normal testis.

Domain organisation. The cleavage module binding motif (CMBM) mediates recruitment of transcription factors.

Similarity. Belongs to the Integrator subunit 13 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NVM9-1	1	yes
Q9NVM9-2	2

RefSeq proteins (1): NP_060634* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019355	Cell_cycle_regulator_Mat89Bb	Family

Pfam: PF10221

UniProt features (79 total): strand 25, helix 23, sequence conflict 9, mutagenesis site 4, turn 4, region of interest 3, modified residue 3, sequence variant 2, chain 1, cross-link 1, splice variant 1, coiled-coil region 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
8PK5	X-RAY DIFFRACTION	2.5
6SN1	X-RAY DIFFRACTION	2.54
8RC4	ELECTRON MICROSCOPY	3.1
8PK6	X-RAY DIFFRACTION	3.21
9EOC	ELECTRON MICROSCOPY	3.3
8RBZ	ELECTRON MICROSCOPY	3.7
9EP1	ELECTRON MICROSCOPY	4
9FA4	ELECTRON MICROSCOPY	4
9FA7	ELECTRON MICROSCOPY	4
8RBX	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NVM9-F1	78.67	0.51

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 (4): 611, 623, 626, 678

Mutagenesis-validated functional residues (4):

Position	Phenotype
123–127	abolished interaction with transcription factor znf655.
174–178	abolished interaction with transcription factor znf655.
345–353	abolished interaction with transcription factors.
577–582	loss of nuclear location. location is mainly cytoplasmic or diffuse. loss of dynein recruitment to nuclear envelope.

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6807505	RNA polymerase II transcribes snRNA genes
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)

MSigDB gene sets: 181 (showing top): GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GGGTGGRR_PAX4_03, FOXD3_01, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, chr12p11, GOBP_RNA_SURVEILLANCE, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_CILIUM_MOVEMENT, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_REGULATION_OF_REPRODUCTIVE_PROCESS, GOBP_DNA_TEMPLATED_TRANSCRIPTION_INITIATION, GOBP_TRANSCRIPTION_INITIATION_AT_RNA_POLYMERASE_II_PROMOTER, GOBP_MITOTIC_CELL_CYCLE, DODD_NASOPHARYNGEAL_CARCINOMA_UP

GO Biological Process (10): mitotic spindle organization (GO:0007052), regulation of mitotic cell cycle (GO:0007346), snRNA processing (GO:0016180), flagellated sperm motility (GO:0030317), regulation of transcription elongation by RNA polymerase II (GO:0034243), cell division (GO:0051301), centrosome localization (GO:0051642), regulation of fertilization (GO:0080154), protein localization to nuclear envelope (GO:0090435), RNA polymerase II transcription initiation surveillance (GO:0160240)

GO Molecular Function (2): DNA-binding transcription factor binding (GO:0140297), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604), integrator complex (GO:0032039), INTAC complex (GO:0160232)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Gene expression (Transcription)	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mitotic cell cycle	2
cellular anatomical structure	2
nuclear protein-containing complex	2
spindle organization	1
microtubule cytoskeleton organization involved in mitosis	1
regulation of cell cycle	1
RNA processing	1
snRNA metabolic process	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
transcription elongation by RNA polymerase II	1
regulation of DNA-templated transcription elongation	1
cellular process	1
microtubule organizing center localization	1
fertilization	1
regulation of reproductive process	1
protein localization to nucleus	1
transcription initiation at RNA polymerase II promoter	1
nuclear RNA surveillance	1
transcription factor binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
nucleoplasm	1
intracellular membraneless organelle	1
integrator complex	1

Protein interactions and networks

STRING

1059 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
INTS13	INTS14	Q96SY0	955
INTS13	INTS9	Q9NV88	745
INTS13	INTS1	Q8N201	734
INTS13	INTS11	Q5TA45	732
INTS13	INTS8	Q75QN2	722
INTS13	GOLT1B	Q9Y3E0	720
INTS13	INTS4	Q96HW7	717
INTS13	INTS3	Q68E01	710
INTS13	INTS5	Q6P9B9	692
INTS13	INTS2	Q9H0H0	664
INTS13	NAB2	Q15742	636
INTS13	INTS10	Q9NVR2	623
INTS13	INTS12	Q96CB8	616
INTS13	INTS7	Q9NVH2	606
INTS13	INTS6	Q9UL03	570

IntAct

81 interactions, top by confidence:

A	B	Type	Score
INTS10	INTS14	psi-mi:“MI:0915”(physical association)	0.900
INTS11	INTS4	psi-mi:“MI:0915”(physical association)	0.860
GDI1	RAB4A	psi-mi:“MI:0914”(association)	0.820
INTS13	INTS14	psi-mi:“MI:0915”(physical association)	0.810
INTS14	INTS13	psi-mi:“MI:0915”(physical association)	0.810
INTS13	INTS14	psi-mi:“MI:0407”(direct interaction)	0.810
INTS13	INTS14	psi-mi:“MI:0914”(association)	0.810
INTS14	INTS13	psi-mi:“MI:0914”(association)	0.810
INTS10	INTS11	psi-mi:“MI:0915”(physical association)	0.740
INTS13	INTS11	psi-mi:“MI:0915”(physical association)	0.690
INTS13	INTS11	psi-mi:“MI:0914”(association)	0.690
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
INTS13	ZNF655	psi-mi:“MI:0915”(physical association)	0.550
PPP2R1A	ENSA	psi-mi:“MI:0914”(association)	0.530

BioGRID (84): ZNF655 (Two-hybrid), ASUN (Co-fractionation), C7orf26 (Co-fractionation), DDX26B (Co-fractionation), INTS1 (Co-fractionation), INTS2 (Co-fractionation), INTS4 (Co-fractionation), INTS7 (Co-fractionation), SNX2 (Co-fractionation), VWA9 (Co-fractionation), ASUN (Affinity Capture-MS), ASUN (Affinity Capture-MS), ASUN (Affinity Capture-MS), ASUN (Affinity Capture-MS), ASUN (Affinity Capture-MS)

ESM2 similar proteins: A2A9C3, A2RRP1, A4FUC0, F1PLN3, O75153, O76024, O88480, P03271, P03272, P03273, P12539, P12540, P48752, P56695, P82649, P82650, P82918, P82924, P83565, Q1T765, Q1XHY1, Q32LL9, Q5EA18, Q5R7X0, Q5SW19, Q5T011, Q5TM62, Q5U2W4, Q5ZI69, Q5ZKP2, Q6AXT0, Q6AXZ5, Q6DIK0, Q6GLY5, Q6NUV0, Q767K8, Q80UJ7, Q8BGW1, Q8QZV7, Q8VE18

Diamond homologs: B3LVQ1, B3P100, B4GFN8, B4IBY5, B4JHB4, B4K5S8, B4LWT5, B4NIM7, B4PR20, B4QX59, Q295U5, Q6DIK0, Q6GLY5, Q8QZV7, Q9NVM9, Q9VEX5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
INTS13	“form complex”	“Integrator complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 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
RNA polymerase II transcribes snRNA genes	7	18.9×	4e-05
Regulation of RUNX2 expression and activity	5	15.9×	1e-03
Degradation of beta-catenin by the destruction complex	5	15.2×	1e-03
HIV Life Cycle	5	14.1×	1e-03
HIV Infection	6	12.5×	1e-03
mRNA Polyadenylation	5	7.7×	7e-03
mRNA Splicing - Major Pathway	8	7.7×	1e-03
Separation of Sister Chromatids	7	7.5×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
RNA polymerase II transcription initiation surveillance	6	88.7×	2e-08
regulation of transcription elongation by RNA polymerase II	5	66.9×	2e-06
chromatin remodeling	7	8.5×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

2994 predictions. Top by Δscore:

Variant	Effect	Δscore
12:26905532:CCATC:C	acceptor_gain	1.0000
12:26905533:CATC:C	acceptor_gain	1.0000
12:26905533:CATCC:C	acceptor_gain	1.0000
12:26905535:TC:T	acceptor_gain	1.0000
12:26905536:CC:C	acceptor_gain	1.0000
12:26905536:CCTGA:C	acceptor_loss	1.0000
12:26905537:C:CC	acceptor_gain	1.0000
12:26905542:A:AC	acceptor_gain	1.0000
12:26906298:AAAC:A	donor_gain	1.0000
12:26906304:ATTTT:A	donor_gain	1.0000
12:26906308:T:A	donor_gain	1.0000
12:26906450:T:C	acceptor_gain	1.0000
12:26911173:CTTA:C	donor_loss	1.0000
12:26911174:TTAC:T	donor_loss	1.0000
12:26911175:TA:T	donor_loss	1.0000
12:26911177:CCTTT:C	donor_loss	1.0000
12:26911318:C:CC	acceptor_gain	1.0000
12:26911319:T:C	acceptor_gain	1.0000
12:26911319:T:TC	acceptor_gain	1.0000
12:26911321:T:C	acceptor_gain	1.0000
12:26911321:T:TC	acceptor_gain	1.0000
12:26913481:T:TA	donor_gain	1.0000
12:26913530:C:A	donor_gain	1.0000
12:26913540:T:TA	donor_gain	1.0000
12:26915995:GTCTT:G	donor_loss	1.0000
12:26915996:TCTTA:T	donor_loss	1.0000
12:26915997:CTTA:C	donor_loss	1.0000
12:26915998:TTACT:T	donor_loss	1.0000
12:26915999:TACTG:T	donor_loss	1.0000
12:26916000:A:AC	donor_gain	1.0000

AlphaMissense

4664 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:26906329:A:G	L685P	1.000
12:26906329:A:T	L685Q	1.000
12:26906367:A:C	F672L	1.000
12:26906367:A:T	F672L	1.000
12:26906368:A:G	F672S	1.000
12:26906369:A:G	F672L	1.000
12:26906414:A:G	W657R	1.000
12:26906414:A:T	W657R	1.000
12:26913592:A:G	L557P	1.000
12:26913604:A:T	V553D	1.000
12:26913643:A:T	V540D	1.000
12:26913646:A:G	L539P	1.000
12:26913657:T:A	E535D	1.000
12:26913657:T:G	E535D	1.000
12:26913658:T:A	E535V	1.000
12:26913658:T:G	E535A	1.000
12:26913659:C:T	E535K	1.000
12:26913663:C:A	W533C	1.000
12:26913663:C:G	W533C	1.000
12:26913664:C:G	W533S	1.000
12:26913665:A:G	W533R	1.000
12:26913665:A:T	W533R	1.000
12:26913667:A:C	M532R	1.000
12:26913667:A:T	M532K	1.000
12:26913673:C:G	R530P	1.000
12:26913674:G:T	R530S	1.000
12:26913677:A:C	Y529D	1.000
12:26913677:A:G	Y529H	1.000
12:26913687:T:A	R525S	1.000
12:26913687:T:G	R525S	1.000

dbSNP variants (sampled 300 via entrez): RS1000029575 (12:26933039 T>C), RS1000094243 (12:26932489 C>A), RS1000146923 (12:26934263 G>A), RS1000278512 (12:26914232 G>A), RS1000339530 (12:26906569 C>T), RS1000557066 (12:26912784 G>A), RS1000609398 (12:26912504 T>C), RS1000620371 (12:26926158 T>C), RS1000719707 (12:26938296 C>G,T), RS1000774627 (12:26931789 A>G), RS1000799791 (12:26905796 T>C), RS1000873979 (12:26926743 T>C), RS1000994013 (12:26925914 T>A), RS1001148961 (12:26919777 G>C,T), RS1001242059 (12:26911930 T>C)

Disease associations

OMIM: gene MIM:615079 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
orofaciodigital syndrome	Strong	Autosomal recessive

Mondo (1): orofaciodigital syndrome (MONDO:0015375)

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST009391_1971	Metabolite levels	6.000000e-06
GCST009391_444	Metabolite levels	3.000000e-07
GCST012489_156	Heel bone mineral density x serum urate levels interaction	4.000000e-08
GCST90002392_378	Mean corpuscular volume	4.000000e-19

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0010541	trimethylamine-N-oxide measurement
EFO:0010386	phosphatidylcholine 38:4 measurement
EFO:0004531	urate measurement
EFO:0009270	heel bone mineral density

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D009958	Orofaciodigital Syndromes	C05.116.099.370.652; C05.660.207.700; C16.131.077.676; C16.131.260.830.670; C16.131.621.207.700; C16.320.180.830.670; C16.320.714

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Hydrogen Peroxide	affects expression, increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases oxidation, increases abundance, affects cotreatment	1
bisphenol A	increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
coumarin	increases phosphorylation	1
methacrylaldehyde	increases oxidation, increases abundance, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
jinfukang	decreases expression	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
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Ivermectin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	decreases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01962129	Not specified	UNKNOWN	Clinical and Molecular Characterisation of Orofaciodigital Syndromes and Other Clinical Phenotypes Secondary to Mutations in the OFD1 Gene