LMO7

Summary

LMO7 (LIM domain 7, HGNC:6646) is a protein-coding gene on chromosome 13q22.2, encoding LIM domain only protein 7 (Q8WWI1).

This gene encodes a protein containing a calponin homology (CH) domain, a PDZ domain, and a LIM domain, and may be involved in protein-protein interactions. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene, however, the full-length nature of some variants is not known.

Source: NCBI Gene 4008 — RefSeq curated summary.

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 334 total
• MANE Select transcript: NM_001306080

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6646
Approved symbol	LMO7
Name	LIM domain 7
Location	13q22.2
Locus type	gene with protein product
Status	Approved
Aliases	FBX20, KIAA0858
Ensembl gene	ENSG00000136153
Ensembl biotype	protein_coding
OMIM	604362
Entrez	4008

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 26 protein_coding, 4 protein_coding_CDS_not_defined, 4 retained_intron

ENST00000321797, ENST00000341547, ENST00000357063, ENST00000377499, ENST00000377534, ENST00000447038, ENST00000465261, ENST00000465309, ENST00000467686, ENST00000482116, ENST00000485987, ENST00000489941, ENST00000497947, ENST00000524651, ENST00000525107, ENST00000525373, ENST00000525914, ENST00000526202, ENST00000526371, ENST00000526528, ENST00000532377, ENST00000532785, ENST00000533299, ENST00000533305, ENST00000533809, ENST00000534657, ENST00000605961, ENST00000715261, ENST00000891623, ENST00000891624, ENST00000891625, ENST00000891626, ENST00000891627, ENST00000891628

RefSeq mRNA: 8 — MANE Select: NM_001306080 NM_001306080, NM_001330583, NM_001366632, NM_001366633, NM_001366634, NM_001366636, NM_005358, NM_015842

CCDS: CCDS53876, CCDS81773, CCDS81774, CCDS9454

Canonical transcript exons

ENST00000377534 — 31 exons

Exon	Start	End
ENSE00000923706	75823565	75823873
ENSE00001003785	75819393	75819535
ENSE00001151303	75835233	75835339
ENSE00001151330	75809154	75809183
ENSE00001151379	75842851	75842916
ENSE00001151396	75838140	75838196
ENSE00001155340	75821177	75821609
ENSE00001191079	75841628	75841983
ENSE00001191432	75807480	75808199
ENSE00001680835	75849079	75849292
ENSE00002170185	75845327	75845379
ENSE00003481492	75795401	75795431
ENSE00003484797	75833051	75833165
ENSE00003490646	75800684	75800882
ENSE00003498773	75855260	75855368
ENSE00003500419	75796636	75796749
ENSE00003520161	75760932	75761038
ENSE00003528336	75804289	75804541
ENSE00003543340	75727029	75727098
ENSE00003583377	75857921	75859866
ENSE00003588156	75853092	75853388
ENSE00003639868	75836397	75836457
ENSE00003653733	75834226	75834387
ENSE00003682507	75713182	75713252
ENSE00003692471	75856506	75856608
ENSE00003695898	75840391	75840495
ENSE00003733727	75636330	75636726
ENSE00003787309	75841109	75841201
ENSE00003787805	75840085	75840110
ENSE00003788309	75805479	75805760
ENSE00003791644	75817161	75817278

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 99.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 37.4179 / max 1403.3001, expressed in 1570 samples.

FANTOM5 promoters (38 alternative TSS)

Promoter ID	TPM avg	Samples expressed
135403	20.1501	1301
135420	4.5515	477
135406	1.0408	315
135402	0.9280	573
135429	0.8159	187
135434	0.8077	111
135417	0.7901	227
135437	0.7895	377
135433	0.7823	152
135404	0.7793	322

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	99.31	gold quality
lower esophagus mucosa	UBERON:0035834	99.29	gold quality
apex of heart	UBERON:0002098	98.96	gold quality
right lung	UBERON:0002167	98.70	gold quality
upper lobe of left lung	UBERON:0008952	98.39	gold quality
right atrium auricular region	UBERON:0006631	98.21	gold quality
calcaneal tendon	UBERON:0003701	97.79	gold quality
left lobe of thyroid gland	UBERON:0001120	97.46	gold quality
right lobe of thyroid gland	UBERON:0001119	97.41	gold quality
tibial nerve	UBERON:0001323	97.31	gold quality
cortical plate	UBERON:0005343	97.10	gold quality
upper lobe of lung	UBERON:0008948	96.78	gold quality
metanephros cortex	UBERON:0010533	96.77	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.76	gold quality
stromal cell of endometrium	CL:0002255	96.27	gold quality
heart left ventricle	UBERON:0002084	96.23	gold quality
gastrocnemius	UBERON:0001388	96.11	gold quality
mucosa of transverse colon	UBERON:0004991	95.93	gold quality
descending thoracic aorta	UBERON:0002345	95.87	gold quality
muscle of leg	UBERON:0001383	95.77	gold quality
esophagus mucosa	UBERON:0002469	95.76	gold quality
thyroid gland	UBERON:0002046	95.60	gold quality
minor salivary gland	UBERON:0001830	95.53	gold quality
cardiac ventricle	UBERON:0002082	95.36	gold quality
thoracic aorta	UBERON:0001515	95.33	gold quality
ascending aorta	UBERON:0001496	95.29	gold quality
rectum	UBERON:0001052	95.27	gold quality
gall bladder	UBERON:0002110	95.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.13	gold quality
right lobe of liver	UBERON:0001114	94.93	gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	2480.79
E-GEOD-131882	yes	2298.07
E-CURD-114	yes	43.86
E-HCAD-1	yes	23.81
E-MTAB-8410	yes	22.76
E-GEOD-130148	yes	13.52
E-GEOD-86618	no	1872.48
E-CURD-11	no	1132.32
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): SRF, TCF12

miRNA regulators (miRDB)

100 targeting LMO7, 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-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-205-3P	99.92	69.92	3165

Literature-anchored findings (GeneRIF, showing 14)

• Lmo7 positively regulates many EDMD-relevant genes (including emerin), and is feedback-regulated by binding to emerin. (PMID:17067998)
• functional interaction between emerin and Lmo7 is crucial for temporally regulating the expression of key myogenic differentiation genes. (PMID:21525034)
• show that LMO7 is upregulated in the stroma of invasive breast carcinoma in a manner that correlates with the increased expression of serum response factor target genes (PMID:21670154)
• Data suggest that Lmo7 is localized at the perinuclear region and in fibril-like structures along subsarcolemma of human skeletal myoblasts whereas in human myotubes Lmo7 is found diffuse throughout the cytoplasm. (PMID:26786059)
• study suggested that the LMO7 gene may play an important role in the pathogenesis of DCM in the Han Chinese population. (PMID:27988857)
• The miR-96-LMO7 axis may be a therapeutic target for lung cancer patients, and new diagnostic or therapeutic strategies could be developed by targeting the miR-96-LMO7 axis. (PMID:28026121)
• Data suggest that LMO7 interacts with MAD1 during spindle assembly phase of mitosis; LMO7 plays role in control of mitosis progression and exerts effect on spindle assembly checkpoint; LMO7 colocalizes with actin filaments; LMO7 does not colocalize with MAD1 at kinetochores in prometaphase nor at spindle poles in metaphase. (LMO7 = LIM domain only protein-7; MAD1 = mitotic spindle assembly checkpoint protein MAD1) (PMID:29158164)
• the LMO7-BRAF fusion behaves as an oncogenic alteration in papillary thyroid carcinoma (PMID:29768105)
• LMO7 and LIMCH1 co-localized and co-immunoprecipitated. (PMID:30429017)
• New Findings on LMO7 Transcripts, Proteins and Regulatory Regions in Human and Vertebrate Model Organisms and the Intracellular Distribution in Skeletal Muscle Cells. (PMID:34884689)
• Novel Long Non-Coding RNA (lncRNA) Transcript AL137782.1 Promotes the Migration of Normal Lung Epithelial Cells through Positively Regulating LMO7. (PMID:37762205)
• Exosome-transmitted circular RNA circ-LMO7 facilitates the progression of osteosarcoma by regulating miR-21-5p/ARHGAP24 axis. (PMID:38742566)
• Immunoreactivity of LMO7 and other molecular markers as potential prognostic factors in oropharyngeal squamous cell carcinoma. (PMID:38918827)
• Role of LMO7 in cancer (Review). (PMID:38994754)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lmo7a	ENSDARG00000004930
danio_rerio	lmo7b	ENSDARG00000053535
mus_musculus	Lmo7	ENSMUSG00000033060
rattus_norvegicus	Lmo7	ENSRNOG00000060775
caenorhabditis_elegans		WBGENE00017904

Paralogs (1): LIMCH1 (ENSG00000064042)

Protein

Protein identifiers

LIM domain only protein 7 — Q8WWI1 (reviewed: Q8WWI1)

Alternative names: F-box only protein 20, LOMP

All UniProt accessions (21): A0A0A0MTE2, A0A1P7ZIM8, A0A8V8TKQ1, A0AAQ5BIH2, Q8WWI1, E9PJ10, E9PK58, E9PLU6, E9PMJ6, E9PMP7, E9PMS6, E9PMT2, E9PRE3, E9PRJ0, F8WD26, H0Y424, H0YDG6, H0YDQ3, H0YE95, J3KP06, U3KQE6

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Widely expressed. Isoform 2 and isoform 4 are predominantly expressed in brain.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8WWI1-1	1	yes
Q8WWI1-2	2
Q8WWI1-3	3
Q8WWI1-4	4
Q8WWI1-5	5

RefSeq proteins (8): NP_001293009, NP_001317512, NP_001353561, NP_001353562, NP_001353563, NP_001353565, NP_005349, NP_056667 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR001715	CH_dom	Domain
IPR001781	Znf_LIM	Domain
IPR003096	SM22_calponin	Family
IPR029978	LMO-7	Family
IPR031865	DUF4757	Domain
IPR036034	PDZ_sf	Homologous_superfamily
IPR036872	CH_dom_sf	Homologous_superfamily

Pfam: PF00307, PF00412, PF00595, PF15949

UniProt features (92 total): modified residue 46, compositionally biased region 16, splice variant 6, sequence conflict 5, strand 5, region of interest 4, domain 3, sequence variant 3, helix 2, chain 1, cross-link 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2EAQ	X-RAY DIFFRACTION	1.46

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWI1-F1	50.94	0.04

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 (47): 185, 246, 257, 276, 342, 704, 706, 709, 751, 805, 867, 873, 879, 895, 913, 919, 926, 932, 949, 956 …

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

ID	Pathway
R-HSA-8951664	Neddylation
R-HSA-9725370	Signaling by ALK fusions and activated point mutants
R-HSA-983168	Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1280218	Adaptive Immune System
R-HSA-1643685	Disease
R-HSA-168256	Immune System
R-HSA-392499	Metabolism of proteins
R-HSA-5663202	Diseases of signal transduction by growth factor receptors and second messengers
R-HSA-597592	Post-translational protein modification
R-HSA-9700206	Signaling by ALK in cancer
R-HSA-983169	Class I MHC mediated antigen processing & presentation

MSigDB gene sets: 220 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOCC_CELL_SURFACE, AAAYRNCTG_UNKNOWN, YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN, BROWNE_HCMV_INFECTION_48HR_DN, UEDA_PERIFERAL_CLOCK, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP, GROSS_HYPOXIA_VIA_HIF1A_DN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOCC_APICAL_PLASMA_MEMBRANE

GO Biological Process (6): protein ubiquitination (GO:0016567), regulation of signaling (GO:0023051), regulation of cell adhesion (GO:0030155), positive regulation of transcription by RNA polymerase II (GO:0045944), positive regulation of macromolecule metabolic process (GO:0010604), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (3): ubiquitin-protein transferase activity (GO:0004842), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (10): ubiquitin ligase complex (GO:0000151), nucleus (GO:0005634), nuclear envelope (GO:0005635), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), focal adhesion (GO:0005925), cell surface (GO:0009986), apical plasma membrane (GO:0016324), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-8 pathways:

Category	Pathways
Post-translational protein modification	1
Signaling by ALK in cancer	1
Class I MHC mediated antigen processing & presentation	1
Immune System	1
Disease	1
Metabolism of proteins	1
Diseases of signal transduction by growth factor receptors and second messengers	1
Adaptive Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
intracellular membrane-bounded organelle	2
cytoplasm	2
protein modification by small protein conjugation	1
signaling	1
regulation of biological process	1
cell adhesion	1
regulation of cellular process	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
positive regulation of metabolic process	1
macromolecule metabolic process	1
regulation of macromolecule metabolic process	1
regulation of metabolic process	1
primary metabolic process	1
ubiquitin-like protein transferase activity	1
cation binding	1
binding	1
intracellular protein-containing complex	1
transferase complex	1
nucleus	1
endomembrane system	1
organelle envelope	1
intracellular anatomical structure	1
cell-substrate junction	1
apical part of cell	1
plasma membrane region	1

Protein interactions and networks

STRING

1574 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LMO7	EMD	P50402	990
LMO7	COMMD6	Q7Z4G1	864
LMO7	UCHL3	P15374	856
LMO7	AFDN	P55196	833
LMO7	NECTIN1	Q15223	687
LMO7	EDNRB	P24530	657
LMO7	UCHL1	P09936	638
LMO7	CDH1	P12830	527
LMO7	SSX2IP	Q9Y2D8	526
LMO7	CENPF	P49454	514
LMO7	ACTN4	O43707	498
LMO7	JUN	P05412	493
LMO7	SKP1	P34991	474
LMO7	FBXO48	Q5FWF7	458
LMO7	SOCS3	O14543	444

IntAct

147 interactions, top by confidence:

A	B	Type	Score
SYTL5	RAB27B	psi-mi:“MI:0914”(association)	0.850
YWHAQ	WDR62	psi-mi:“MI:0914”(association)	0.830
YWHAH	ABLIM1	psi-mi:“MI:0914”(association)	0.800
GTF2H5	GTF2H2	psi-mi:“MI:0914”(association)	0.800
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAB	BLTP3B	psi-mi:“MI:0914”(association)	0.610
YWHAG	SHTN1	psi-mi:“MI:0914”(association)	0.560
LMO7	YWHAZ	psi-mi:“MI:0915”(physical association)	0.560
YWHAZ	BLTP3B	psi-mi:“MI:0914”(association)	0.530
EAPP	SNRNP200	psi-mi:“MI:0914”(association)	0.530
CDR2	IGSF3	psi-mi:“MI:0914”(association)	0.530
KCTD17	CBX4	psi-mi:“MI:0914”(association)	0.530
PIP	TBKBP1	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
YWHAQ	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
ATP2B4	LMO7	psi-mi:“MI:0407”(direct interaction)	0.440
FRMPD4	LMO7	psi-mi:“MI:0407”(direct interaction)	0.440
TAMALIN	LMO7	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (255): LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS), LMO7 (Co-fractionation), LMO7 (Biochemical Activity), LMO7 (Proximity Label-MS), LMO7 (Proximity Label-MS), LMO7 (Proximity Label-MS), LMO7 (Proximity Label-MS), LMO7 (Proximity Label-MS), LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS), LMO7 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8HBI7, A0A1L8HJK9, A0A1L8HTT5, A4QP16, A6NP61, B2RVL6, C0SPG1, C3VD30, K7SGN7, O54880, P56163, Q1XFL1, Q29RJ0, Q2KI52, Q32L09, Q3V0J4, Q4R2Y2, Q4R739, Q58D79, Q5RAK6, Q5TKR9, Q5VWQ0, Q6PDK8, Q768S4, Q7T3T8, Q7T3T9, Q80T69, Q86US8, Q86Y01, Q8AW93, Q8BMD7, Q8BRB7, Q8BZ21, Q8CAK3, Q8CDN1, Q8HXK7, Q8K3Y6, Q8N2G6, Q8N9V6, Q8TE76

Diamond homologs: B9EUM5, B9G8P1, O14188, O75427, P14318, P15498, P19966, P26932, P27870, P31232, P37397, P37802, P37803, P37804, P37805, P51911, P54100, Q01995, Q08091, Q08092, Q08093, Q08094, Q08290, Q08DN7, Q14155, Q15052, Q15417, Q24799, Q2HJ38, Q32L92, Q3KQW7, Q3SYU6, Q3UH68, Q3UMG5, Q3ZBY2, Q4R5J4, Q54TK8, Q55DD4, Q55E26, Q55GV9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 159 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
Activation of BAD and translocation to mitochondria	7	49.8×	4e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	44.0×	9e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	44.0×	9e-09
Activation of BH3-only proteins	7	32.5×	8e-08
RHO GTPases activate PKNs	9	26.7×	4e-09
Signaling by RAS mutants	5	19.8×	1e-04
Intrinsic Pathway for Apoptosis	7	19.2×	3e-06
RHO GTPases activate IQGAPs	5	16.2×	3e-04

GO biological processes:

GO term	Partners	Fold	FDR
intracellular protein localization	11	8.1×	1e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	242
Likely benign	28
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

6461 predictions. Top by Δscore:

Variant	Effect	Δscore
13:75713181:GGCA:G	acceptor_gain	1.0000
13:75713249:GTGA:G	donor_gain	1.0000
13:75713253:G:GG	donor_gain	1.0000
13:75727026:CAGTT:C	acceptor_loss	1.0000
13:75727027:A:AG	acceptor_gain	1.0000
13:75727027:AGTTT:A	acceptor_gain	1.0000
13:75727028:G:GT	acceptor_gain	1.0000
13:75727028:GT:G	acceptor_gain	1.0000
13:75727028:GTT:G	acceptor_gain	1.0000
13:75727028:GTTT:G	acceptor_gain	1.0000
13:75727028:GTTTG:G	acceptor_gain	1.0000
13:75727094:GATTG:G	donor_gain	1.0000
13:75727096:TTG:T	donor_gain	1.0000
13:75727097:TGGTA:T	donor_loss	1.0000
13:75727098:GGT:G	donor_loss	1.0000
13:75727099:G:A	donor_loss	1.0000
13:75727099:G:GG	donor_gain	1.0000
13:75727100:T:A	donor_loss	1.0000
13:75760930:A:AG	acceptor_gain	1.0000
13:75760931:G:GG	acceptor_gain	1.0000
13:75760931:GGATA:G	acceptor_gain	1.0000
13:75761034:GTCAA:G	donor_gain	1.0000
13:75761035:TC:T	donor_gain	1.0000
13:75761035:TCAA:T	donor_gain	1.0000
13:75761035:TCAAG:T	donor_loss	1.0000
13:75761036:CAA:C	donor_gain	1.0000
13:75761037:AA:A	donor_gain	1.0000
13:75761037:AAGTA:A	donor_loss	1.0000
13:75761038:AGTA:A	donor_loss	1.0000
13:75761039:G:GG	donor_gain	1.0000

AlphaMissense

10728 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000004623 (13:75823392 A>G), RS1000009905 (13:75622796 C>A,G), RS1000028093 (13:75749746 T>TTTAC), RS1000035944 (13:75855606 A>G), RS1000047991 (13:75743616 A>G,T), RS1000052381 (13:75633110 G>A), RS1000055001 (13:75666295 A>G), RS1000061096 (13:75723618 C>G,T), RS1000066357 (13:75812150 G>C), RS1000070732 (13:75659487 T>G), RS1000075172 (13:75782690 G>A,T), RS1000086223 (13:75707997 T>G), RS1000091603 (13:75723351 T>C), RS1000092848 (13:75695530 A>G), RS1000151493 (13:75683067 T>C,G)

Disease associations

OMIM: gene MIM:604362 | disease phenotypes: MIM:600057

GenCC curated gene-disease

Mondo (1): bladder exstrophy-epispadias-cloacal exstrophy complex (MONDO:0700039)

Orphanet (1): Classic bladder exstrophy (Orphanet:93930)

HPO phenotypes

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

GWAS associations

19 associations (top):

Study	Trait	p-value
GCST001255_2	Type 1 diabetes	6.000000e-11
GCST003783_10	Multiple system atrophy (pathologically confirmed)	5.000000e-06
GCST005023_35	Initial pursuit acceleration	7.000000e-08
GCST005026_20	Initial pursuit acceleration in psychotic disorders	4.000000e-08
GCST005026_7	Initial pursuit acceleration in psychotic disorders	6.000000e-09
GCST005407_4	Glaucoma (primary open-angle)	3.000000e-09
GCST005580_30	Intraocular pressure	2.000000e-13
GCST005580_42	Intraocular pressure	8.000000e-13
GCST006394_94	Intraocular pressure	2.000000e-12
GCST006412_83	Intraocular pressure	1.000000e-10
GCST007208_4	Obsessive-compulsive disorder	3.000000e-06
GCST009722_6	Glaucoma (multi-trait analysis)	1.000000e-12
GCST009725_35	Intraocular pressure	1.000000e-12
GCST010302_14	Cutaneous melanoma or hair colour	9.000000e-09
GCST011438_13	Glaucoma (primary open-angle)	5.000000e-06
GCST011439_2	Glaucoma (primary open-angle)	3.000000e-08
GCST012442_18	Age-related hearing impairment	2.000000e-09
GCST90002390_193	Mean corpuscular hemoglobin	1.000000e-10
GCST90011770_66	Glaucoma (primary open-angle)	3.000000e-16

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0008434	initial pursuit acceleration
EFO:0004695	intraocular pressure measurement
EFO:0003924	hair color
EFO:0004527	mean corpuscular hemoglobin

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, increases expression, affects expression	6
sodium arsenite	affects methylation, decreases expression, increases abundance, increases stability	5
Tetrachlorodibenzodioxin	decreases reaction, increases expression, affects expression	5
Tobacco Smoke Pollution	affects expression, decreases expression, increases expression	3
trichostatin A	increases expression	2
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
bisphenol S	affects expression, affects cotreatment, increases methylation	2
Air Pollutants	decreases expression, affects cotreatment, increases abundance, increases oxidation	2
Arsenic	decreases expression, increases abundance	2
Estradiol	decreases expression, decreases reaction, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
Cyclosporine	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
geldanamycin	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	affects cotreatment, increases methylation	1
sodium arsenate	decreases expression, increases abundance	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression	1
beta-lapachone	decreases expression, increases expression	1
arsenite	affects binding, decreases reaction	1
ochratoxin A	decreases expression	1
aflatoxin B2	decreases methylation	1
coumarin	affects phosphorylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1

Clinical trials (associated diseases)

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