LIMCH1

Summary

LIMCH1 (LIM and calponin homology domains 1, HGNC:29191) is a protein-coding gene on chromosome 4p13, encoding LIM and calponin homology domains-containing protein 1 (Q9UPQ0). Actin stress fibers-associated protein that activates non-muscle myosin IIa.

Enables myosin II head/neck binding activity. Involved in several processes, including cytoplasmic actin-based contraction involved in cell motility; positive regulation of stress fiber assembly; and regulation of focal adhesion assembly. Located in myosin II complex and stress fiber.

Source: NCBI Gene 22998 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 214 total
• MANE Select transcript: NM_001330672

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29191
Approved symbol	LIMCH1
Name	LIM and calponin homology domains 1
Location	4p13
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP686A01247, LIMCH1A, LMO7B
Ensembl gene	ENSG00000064042
Ensembl biotype	protein_coding
OMIM	617750
Entrez	22998

Gene structure

Transcript identifiers

Ensembl transcripts: 175 — 170 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000313860, ENST00000381753, ENST00000396595, ENST00000446625, ENST00000503057, ENST00000505705, ENST00000508466, ENST00000508501, ENST00000509277, ENST00000509454, ENST00000509638, ENST00000511424, ENST00000511496, ENST00000512228, ENST00000512632, ENST00000512820, ENST00000512946, ENST00000513024, ENST00000514096, ENST00000514190, ENST00000515785, ENST00000515847, ENST00000855817, ENST00000855818, ENST00000855819, ENST00000855820, ENST00000855821, ENST00000855822, ENST00000855823, ENST00000855824, ENST00000855825, ENST00000855826, ENST00000855827, ENST00000855828, ENST00000855829, ENST00000855830, ENST00000855831, ENST00000855832, ENST00000855833, ENST00000855834, ENST00000855835, ENST00000855836, ENST00000855837, ENST00000855838, ENST00000855839, ENST00000855840, ENST00000855841, ENST00000855842, ENST00000855843, ENST00000855844, ENST00000944047, ENST00000944048, ENST00000944049, ENST00000944050, ENST00000944051, ENST00000944052, ENST00000944053, ENST00000944054, ENST00000944055, ENST00000944056, ENST00000944057, ENST00000944058, ENST00000944059, ENST00000944060, ENST00000944061, ENST00000944062, ENST00000944063, ENST00000944064, ENST00000944065, ENST00000944066, ENST00000944067, ENST00000944068, ENST00000944069, ENST00000944070, ENST00000944071, ENST00000944072, ENST00000944073, ENST00000944074, ENST00000944075, ENST00000944076, ENST00000944077, ENST00000944078, ENST00000944079, ENST00000944080, ENST00000944081, ENST00000944082, ENST00000944083, ENST00000944084, ENST00000944085, ENST00000944086, ENST00000944087, ENST00000944088, ENST00000944089, ENST00000944090, ENST00000944091, ENST00000944092, ENST00000944093, ENST00000944094, ENST00000944095, ENST00000944096, ENST00000944097, ENST00000944098, ENST00000944099, ENST00000944100, ENST00000944101, ENST00000944102, ENST00000944103, ENST00000944104, ENST00000944105, ENST00000944106, ENST00000944107, ENST00000944108, ENST00000944109, ENST00000944110, ENST00000944111, ENST00000944112, ENST00000944113, ENST00000944114, ENST00000944115, ENST00000944116, ENST00000944117, ENST00000944118, ENST00000944119, ENST00000944120, ENST00000944121, ENST00000944122, ENST00000944123, ENST00000944124, ENST00000944125, ENST00000944126, ENST00000944127, ENST00000944128, ENST00000944129, ENST00000944130, ENST00000944131, ENST00000944132, ENST00000944133, ENST00000944134, ENST00000944135, ENST00000944136, ENST00000944137, ENST00000944138, ENST00000944139, ENST00000944140, ENST00000944141, ENST00000944142, ENST00000944143, ENST00000944144, ENST00000944145, ENST00000944146, ENST00000944147, ENST00000944148, ENST00000944149, ENST00000944150, ENST00000944151, ENST00000944152, ENST00000944153, ENST00000944154, ENST00000944155, ENST00000944156, ENST00000944157, ENST00000944158, ENST00000944159, ENST00000944160, ENST00000944161, ENST00000944162, ENST00000944163, ENST00000944164, ENST00000944165, ENST00000944166, ENST00000944167, ENST00000944168, ENST00000944169, ENST00000944170, ENST00000944171

RefSeq mRNA: 20 — MANE Select: NM_001330672 NM_001112717, NM_001112718, NM_001112719, NM_001112720, NM_001289122, NM_001289124, NM_001330672, NM_001330674, NM_001330784, NM_001330786, NM_001330787, NM_001330788, NM_001330789, NM_001330790, NM_001330791, NM_001330792, NM_001330793, NM_001330982, NM_001330983, NM_014988

CCDS: CCDS33977, CCDS47047, CCDS54763, CCDS54764, CCDS54765, CCDS75119, CCDS75121, CCDS82919, CCDS82920, CCDS87221, CCDS87222

Canonical transcript exons

ENST00000503057 — 32 exons

Exon	Start	End
ENSE00001205284	41638932	41638967
ENSE00001314261	41613466	41613661
ENSE00001597340	41662821	41662984
ENSE00001627319	41689527	41689635
ENSE00001654024	41692282	41692384
ENSE00001657808	41650393	41650608
ENSE00001667844	41661420	41661510
ENSE00001677078	41676382	41676462
ENSE00001681891	41671554	41671594
ENSE00001710033	41644500	41644626
ENSE00001712622	41646123	41646280
ENSE00001721781	41680955	41681059
ENSE00001730971	41666561	41666666
ENSE00001759109	41646485	41646893
ENSE00001772882	41680006	41680098
ENSE00001778948	41685710	41685830
ENSE00001783775	41684397	41684518
ENSE00001787620	41619188	41619440
ENSE00002042029	41697160	41700044
ENSE00002069270	41538157	41538350
ENSE00002127402	41682333	41682460
ENSE00003533088	41605894	41606004
ENSE00003633954	41603875	41603905
ENSE00003676607	41598920	41599026
ENSE00004010800	41631148	41631477
ENSE00004010801	41633548	41633808
ENSE00004010802	41632977	41633085
ENSE00004010803	41626708	41627010
ENSE00004010804	41620424	41620690
ENSE00004010805	41687840	41687917
ENSE00004010806	41632749	41632867
ENSE00004010807	41629492	41629734

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 99.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.4542 / max 1194.0314, expressed in 1185 samples.

FANTOM5 promoters (24 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47474	15.6951	1021
47473	3.4888	803
47490	2.0119	373
47471	1.9349	535
47479	1.7139	363
47475	1.6021	405
47495	1.3296	397
47485	0.7311	191
47489	0.6177	192
47480	0.4660	154

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower lobe of lung	UBERON:0008949	99.37	gold quality
medial globus pallidus	UBERON:0002477	99.22	gold quality
inferior vagus X ganglion	UBERON:0005363	99.15	gold quality
olfactory bulb	UBERON:0002264	99.11	gold quality
globus pallidus	UBERON:0001875	99.10	gold quality
corpus callosum	UBERON:0002336	99.09	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	99.04	gold quality
cortical plate	UBERON:0005343	98.97	gold quality
medulla oblongata	UBERON:0001896	98.64	gold quality
inferior olivary complex	UBERON:0002127	98.54	gold quality
subthalamic nucleus	UBERON:0001906	98.48	gold quality
superior vestibular nucleus	UBERON:0007227	98.36	gold quality
substantia nigra pars reticulata	UBERON:0001966	98.35	gold quality
lateral globus pallidus	UBERON:0002476	98.35	gold quality
Brodmann (1909) area 23	UBERON:0013554	98.30	gold quality
right lung	UBERON:0002167	98.28	gold quality
left ventricle myocardium	UBERON:0006566	98.27	gold quality
substantia nigra pars compacta	UBERON:0001965	98.18	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	98.12	gold quality
ventral tegmental area	UBERON:0002691	98.09	gold quality
heart right ventricle	UBERON:0002080	98.07	gold quality
middle temporal gyrus	UBERON:0002771	98.06	gold quality
tibia	UBERON:0000979	97.90	gold quality
parotid gland	UBERON:0001831	97.85	gold quality
trigeminal ganglion	UBERON:0001675	97.82	gold quality
ventricular zone	UBERON:0003053	97.80	gold quality
CA1 field of hippocampus	UBERON:0003881	97.78	gold quality
dorsal plus ventral thalamus	UBERON:0001897	97.76	gold quality
pigmented layer of retina	UBERON:0001782	97.73	gold quality
retina	UBERON:0000966	97.71	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 11.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	4765.96
E-HCAD-23	yes	2099.07
E-GEOD-114530	yes	408.72
E-CURD-6	yes	317.62
E-HCAD-10	yes	303.13
E-CURD-119	yes	42.38
E-GEOD-135922	yes	39.75
E-GEOD-93593	yes	13.26
E-GEOD-84465	yes	11.40
E-GEOD-130148	yes	9.04
E-GEOD-124858	no	1658.13
E-CURD-112	no	2.98
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting LIMCH1, 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-3646	100.00	73.56	5283
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3613-3P	100.00	76.36	7965
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-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
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-4531	99.99	69.70	3181
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-367-3P	99.98	74.83	1819

Literature-anchored findings (GeneRIF, showing 6)

• Data suggest that LIMCH1 plays a positive role in regulation of NM-II activity through effects on MRLC during cell migration. (PMID:28228547)
• LMO7 and LIMCH1 co-localized and co-immunoprecipitated. (PMID:30429017)
• LIMCH1 is a negative regulator involved in a new molecular mechanism for the pathogenesis of lung cancer with HUWE1 and p53 (PMID:31279706)
• Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. (PMID:31959624)
• A 10-gene prognostic signature points to LIMCH1 and HLA-DQB1 as important players in aggressive cervical cancer disease. (PMID:33723390)
• LIMCH1 as a New Potential Metastasis Predictor in Breast Cancer. (PMID:36444609)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	limch1a	ENSDARG00000074275
danio_rerio	limch1b	ENSDARG00000103774
mus_musculus	Limch1	ENSMUSG00000037736
rattus_norvegicus	Limch1	ENSRNOG00000002318
caenorhabditis_elegans		WBGENE00017904

Paralogs (1): LMO7 (ENSG00000136153)

Protein

Protein identifiers

LIM and calponin homology domains-containing protein 1 — Q9UPQ0 (reviewed: Q9UPQ0)

All UniProt accessions (10): Q9UPQ0, D6R8Y0, D6RD46, D6RGH8, D6RJ93, E7EPK0, E9PDJ9, G5EA03, H0Y8P3, Q6NVB9

UniProt curated annotations — full annotation on UniProt →

Function. Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration.

Subunit / interactions. Interacts with MYH9; independently of the integration of MYH9 into the myosin complex.

Subcellular location. Cytoplasm. Cytoskeleton. Stress fiber.

Similarity. Belongs to the LIMCH1 family.

Isoforms (10)

UniProt ID	Names	Canonical?
Q9UPQ0-1	1	yes
Q9UPQ0-2	2
Q9UPQ0-3	3
Q9UPQ0-4	4
Q9UPQ0-5	5
Q9UPQ0-6	6
Q9UPQ0-7	7
Q9UPQ0-8	8
Q9UPQ0-9	9
Q9UPQ0-10	10

RefSeq proteins (20): NP_001106188, NP_001106189, NP_001106190, NP_001106191, NP_001276051, NP_001276053, NP_001317601, NP_001317603, NP_001317713, NP_001317715, NP_001317716, NP_001317717, NP_001317718, NP_001317719, NP_001317720, NP_001317721, NP_001317722, NP_001317911, NP_001317912, NP_055803 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001715	CH_dom	Domain
IPR001781	Znf_LIM	Domain
IPR001997	Calponin/LIMCH1	Family
IPR003096	SM22_calponin	Family
IPR031865	DUF4757	Domain
IPR036872	CH_dom_sf	Homologous_superfamily

Pfam: PF00307, PF00412, PF15949

UniProt features (75 total): modified residue 34, sequence conflict 12, splice variant 10, compositionally biased region 8, region of interest 5, domain 2, coiled-coil region 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UPQ0-F1	56.48	0.14

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 (34): 169, 177, 192, 201, 204, 207, 215, 217, 226, 231, 233, 297, 303, 313, 377, 402, 471, 472, 516, 518 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 245 (showing top): AAGCAAT_MIR137, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_FOCAL_ADHESION_ASSEMBLY, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, MODULE_503, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GTGCCTT_MIR506, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_CELL_JUNCTION_ORGANIZATION, CATTTCA_MIR203

GO Biological Process (8): positive regulation of protein phosphorylation (GO:0001934), negative regulation of cell migration (GO:0030336), actomyosin structure organization (GO:0031032), positive regulation of stress fiber assembly (GO:0051496), regulation of focal adhesion assembly (GO:0051893), cytoplasmic actin-based contraction involved in cell motility (GO:0060327), positive regulation of macromolecule metabolic process (GO:0010604), regulation of primary metabolic process (GO:0080090)

GO Molecular Function (4): actin binding (GO:0003779), myosin II head/neck binding (GO:0032034), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (5): stress fiber (GO:0001725), actin cytoskeleton (GO:0015629), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), myosin II complex (GO:0016460)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of protein phosphorylation	1
protein phosphorylation	1
positive regulation of protein modification process	1
positive regulation of phosphorylation	1
cell migration	1
regulation of cell migration	1
negative regulation of cell motility	1
actin cytoskeleton organization	1
positive regulation of actin filament bundle assembly	1
stress fiber assembly	1
regulation of stress fiber assembly	1
regulation of cell-matrix adhesion	1
focal adhesion assembly	1
regulation of cell-substrate junction assembly	1
cell motility	1
actin-mediated cell contraction	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
cytoskeletal protein binding	1
myosin head/neck binding	1
myosin II heavy chain binding	1
cation binding	1
binding	1
actomyosin	1
contractile actin filament bundle	1
cytoskeleton	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1
myosin complex	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

70 interactions, top by confidence:

A	B	Type	Score
SYTL5	RAB27B	psi-mi:“MI:0914”(association)	0.850
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
FGL1	LCMT2	psi-mi:“MI:0914”(association)	0.640
TNNI2	TNNC1	psi-mi:“MI:0914”(association)	0.590
CFTR	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
LIMCH1	KLHL15	psi-mi:“MI:0915”(physical association)	0.400
MYH9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
ANLN	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO18A	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
MYO19	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Actb		psi-mi:“MI:0914”(association)	0.350
Calml3	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Myh9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Myo1c	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Kif3c	ARPC1B	psi-mi:“MI:0914”(association)	0.350
Myh9	GOSR1	psi-mi:“MI:0914”(association)	0.350
MYH9	NAP1L1	psi-mi:“MI:0914”(association)	0.350
Myh10	NAP1L1	psi-mi:“MI:0914”(association)	0.350

BioGRID (120): LIMCH1 (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), RFC2 (Affinity Capture-MS), YES1 (Affinity Capture-MS), NAGK (Affinity Capture-MS), GNB4 (Affinity Capture-MS), LIMCH1 (Affinity Capture-RNA), LIMCH1 (Affinity Capture-MS), LIMCH1 (Proximity Label-MS), LIMCH1 (Proximity Label-MS), LIMCH1 (Affinity Capture-MS), LIMCH1 (Affinity Capture-MS), LIMCH1 (Affinity Capture-MS), LIMCH1 (Affinity Capture-MS), LIMCH1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTU1, A2AUY4, B7ZS37, D3Z8Y2, D4A4L4, D4A666, E1B7L7, O46385, O60293, O75152, O95425, P0DQW0, Q08AZ1, Q3KQW7, Q3U1C4, Q3UH68, Q3ZC82, Q4G0F8, Q4V9H5, Q5F3Z9, Q5NBX1, Q5REG6, Q5ZJJ1, Q5ZM88, Q61464, Q62394, Q68FE9, Q6NZF1, Q6PJT7, Q6ZQ03, Q6ZU65, Q76L83, Q7TMD5, Q8BHZ4, Q8BJ05, Q8BLG0, Q8BZ32, Q8C9B9, Q8CCJ9, Q8K298

Diamond homologs: O15231, O95171, Q3KQW7, Q3UH68, Q62394, Q9EQG3, Q9UPQ0, 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, Q3SYU6, Q3UMG5, Q3ZBY2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 85 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
RHO GTPase Effectors	6	8.2×	9e-03
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	9	6.0×	3e-03
Signaling by Rho GTPases	8	5.5×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	167
Likely benign	12
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

6107 predictions. Top by Δscore:

Variant	Effect	Δscore
4:41360935:AGGTA:A	donor_loss	1.0000
4:41360938:T:G	donor_loss	1.0000
4:41494531:TGCA:T	acceptor_loss	1.0000
4:41494532:GCA:G	acceptor_loss	1.0000
4:41494533:CAGC:C	acceptor_loss	1.0000
4:41494534:A:AC	acceptor_loss	1.0000
4:41494534:A:AG	acceptor_gain	1.0000
4:41494535:G:GT	acceptor_gain	1.0000
4:41494535:G:T	acceptor_loss	1.0000
4:41494535:GC:G	acceptor_gain	1.0000
4:41494535:GCA:G	acceptor_gain	1.0000
4:41494535:GCAA:G	acceptor_gain	1.0000
4:41494603:GCGA:G	donor_gain	1.0000
4:41494604:CGAG:C	donor_loss	1.0000
4:41494605:GA:G	donor_gain	1.0000
4:41494605:GAGT:G	donor_loss	1.0000
4:41494606:AG:A	donor_loss	1.0000
4:41494607:G:GG	donor_gain	1.0000
4:41494607:GTA:G	donor_loss	1.0000
4:41494608:TAAGT:T	donor_loss	1.0000
4:41494609:AA:A	donor_loss	1.0000
4:41598916:CTA:C	acceptor_loss	1.0000
4:41598917:TA:T	acceptor_loss	1.0000
4:41598918:A:AG	acceptor_gain	1.0000
4:41598918:AG:A	acceptor_gain	1.0000
4:41598918:AGGAC:A	acceptor_loss	1.0000
4:41598919:G:GA	acceptor_gain	1.0000
4:41598919:GG:G	acceptor_gain	1.0000
4:41598919:GGAC:G	acceptor_gain	1.0000
4:41598919:GGACA:G	acceptor_gain	1.0000

AlphaMissense

9711 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:41646135:T:A	W371R	1.000
4:41646135:T:C	W371R	1.000
4:41689549:T:C	C1013R	1.000
4:41613589:A:C	S204R	0.999
4:41613591:C:A	S204R	0.999
4:41613591:C:G	S204R	0.999
4:41644618:T:A	W364R	0.999
4:41644618:T:C	W364R	0.999
4:41646127:T:C	L368P	0.999
4:41646137:G:C	W371C	0.999
4:41646137:G:T	W371C	0.999
4:41646145:G:C	R374P	0.999
4:41646148:G:C	R375T	0.999
4:41646149:A:C	R375S	0.999
4:41646149:A:T	R375S	0.999
4:41646505:T:C	L426P	0.999
4:41646576:T:C	F450L	0.999
4:41646578:C:A	F450L	0.999
4:41646578:C:G	F450L	0.999
4:41680034:T:C	L799P	0.999
4:41680045:T:A	W803R	0.999
4:41680045:T:C	W803R	0.999
4:41680047:G:C	W803C	0.999
4:41680047:G:T	W803C	0.999
4:41680054:G:C	A806P	0.999
4:41689551:C:G	C1013W	0.999
4:41689627:T:C	C1039R	0.999
4:41689629:T:G	C1039W	0.999
4:41692357:T:C	C1067R	0.999
4:41613508:A:C	S177R	0.998

dbSNP variants (sampled 300 via entrez): RS1000005109 (4:41571370 G>A), RS1000019996 (4:41526935 C>T), RS1000023 (4:41552486 G>A,C,T), RS1000024 (4:41552449 C>G,T), RS1000028708 (4:41386663 G>A,T), RS1000038582 (4:41623080 G>A), RS1000067882 (4:41614264 C>T), RS1000072272 (4:41520498 C>A,T), RS1000087544 (4:41659132 G>A), RS1000100037 (4:41535651 G>A), RS1000100931 (4:41666689 T>A), RS10001276 (4:41584011 A>G), RS10001293 (4:41615181 G>T), RS10001496 (4:41407632 C>T), RS1000156872 (4:41398903 C>G)

Disease associations

OMIM: gene MIM:617750 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002599_7	Longevity (90 years and older)	9.000000e-06
GCST002675_1	Response to statins (LDL cholesterol change)	8.000000e-08
GCST006976_90	Macular thickness	5.000000e-09
GCST008477_38	Emphysema annual change measurement in smokers (adjusted lung density)	6.000000e-06
GCST008745_44	Estimated glomerular filtration rate in non-diabetics	3.000000e-08
GCST008747_185	Estimated glomerular filtration rate	5.000000e-06
GCST009462_53	Optic disc size	4.000000e-08
GCST010727_8	Deep white matter hyperintensities	1.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement
EFO:0007626	emphysema imaging measurement
EFO:0005665	white matter hyperintensity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases expression, affects cotreatment	6
sodium arsenite	increases abundance, affects expression, increases expression, affects methylation, affects cotreatment (+1 more)	5
Estradiol	increases reaction, affects cotreatment, increases expression, decreases expression	4
bisphenol A	affects cotreatment, decreases methylation, decreases expression, increases methylation	3
Arsenic	affects methylation, affects cotreatment, decreases expression, increases abundance, affects expression	3
Tretinoin	decreases expression, increases expression, affects cotreatment	3
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	2
belinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Acrolein	affects cotreatment, increases oxidation, increases abundance	2
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, decreases expression	2
Vehicle Emissions	increases abundance, increases expression, increases methylation	2
Cisplatin	affects response to substance, decreases expression	2
Copper	decreases expression, affects binding, increases expression	2
Ozone	affects cotreatment, increases oxidation, increases abundance	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Silicon Dioxide	decreases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
methylmercuric chloride	increases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
trichostatin A	decreases expression, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
zinc chloride	decreases reaction, increases expression	1
cobaltous chloride	increases expression, decreases reaction	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
ochratoxin A	decreases expression	1
coumarin	affects phosphorylation	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1VT	Abcam HeLa LIMCH1 KO	Cancer cell line	Female
CVCL_SV57	HAP1 LIMCH1 (-) 1	Cancer cell line	Male
CVCL_XQ17	HAP1 LIMCH1 (-) 2	Cancer cell line	Male
CVCL_XQ18	HAP1 LIMCH1 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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