PDLIM1

Summary

PDLIM1 (PDZ and LIM domain 1, HGNC:2067) is a protein-coding gene on chromosome 10q23.33, encoding PDZ and LIM domain protein 1 (O00151). Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton.

This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17.

Source: NCBI Gene 9124 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_020992

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2067
Approved symbol	PDLIM1
Name	PDZ and LIM domain 1
Location	10q23.33
Locus type	gene with protein product
Status	Approved
Aliases	CLP-36, hCLIM1, CLP36
Ensembl gene	ENSG00000107438
Ensembl biotype	protein_coding
OMIM	605900
Entrez	9124

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000329399, ENST00000477757, ENST00000490391, ENST00000492511, ENST00000493949, ENST00000862799, ENST00000862800, ENST00000956300, ENST00000956301

RefSeq mRNA: 1 — MANE Select: NM_020992 NM_020992

CCDS: CCDS7441

Canonical transcript exons

ENST00000329399 — 7 exons

Exon	Start	End
ENSE00001306547	95290820	95291003
ENSE00001454795	95237572	95238111
ENSE00003536983	95238568	95238685
ENSE00003550370	95247215	95247366
ENSE00003591760	95263864	95264063
ENSE00003628669	95268778	95268862
ENSE00003643327	95271633	95271784

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 99.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 104.0691 / max 1185.7155, expressed in 1650 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
110750	78.2296	1610
110751	15.9900	1481
110749	5.2764	1278
110752	3.7028	1299
110753	0.6783	373
110741	0.1920	79

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lower lobe of lung	UBERON:0008949	99.40	gold quality
nasal cavity epithelium	UBERON:0005384	99.37	gold quality
mucosa of urinary bladder	UBERON:0001259	99.29	gold quality
right lung	UBERON:0002167	99.25	gold quality
pericardium	UBERON:0002407	99.25	gold quality
gingival epithelium	UBERON:0001949	99.24	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	99.24	gold quality
upper lobe of lung	UBERON:0008948	99.24	gold quality
palpebral conjunctiva	UBERON:0001812	99.23	gold quality
upper lobe of left lung	UBERON:0008952	99.22	gold quality
gingiva	UBERON:0001828	99.19	gold quality
apex of heart	UBERON:0002098	99.17	gold quality
decidua	UBERON:0002450	99.17	gold quality
pharyngeal mucosa	UBERON:0000355	99.12	gold quality
gastrocnemius	UBERON:0001388	99.12	gold quality
mucosa of transverse colon	UBERON:0004991	99.11	gold quality
peritoneum	UBERON:0002358	99.07	gold quality
omental fat pad	UBERON:0010414	99.07	gold quality
colonic mucosa	UBERON:0000317	99.06	gold quality
left lobe of thyroid gland	UBERON:0001120	99.05	gold quality
heart left ventricle	UBERON:0002084	99.04	gold quality
cardiac ventricle	UBERON:0002082	99.03	gold quality
popliteal artery	UBERON:0002250	99.02	gold quality
vena cava	UBERON:0004087	99.02	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.02	gold quality
tibial artery	UBERON:0007610	99.02	gold quality
epithelium of nasopharynx	UBERON:0001951	99.01	gold quality
aorta	UBERON:0000947	99.00	gold quality
ascending aorta	UBERON:0001496	98.98	gold quality
thoracic aorta	UBERON:0001515	98.97	gold quality

Single-cell (SCXA)

Detected in 32 experiment(s), a significant marker in 28.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	1604.27
E-MTAB-8142	yes	1316.00
E-MTAB-9906	yes	1248.05
E-MTAB-7407	yes	1147.79
E-MTAB-8884	yes	961.79
E-HCAD-8	yes	870.93
E-HCAD-6	yes	572.88
E-MTAB-10042	yes	402.50
E-HCAD-4	yes	97.84
E-HCAD-10	yes	64.75
E-CURD-114	yes	61.26
E-MTAB-10553	yes	49.70
E-CURD-112	yes	48.69
E-HCAD-1	yes	46.71
E-MTAB-6701	yes	43.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting PDLIM1, 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-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-922	99.02	67.23	1838
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-628-5P	98.36	67.74	844
HSA-MIR-219B-5P	97.91	65.80	531
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-4726-5P	97.24	65.67	1299
HSA-MIR-1287-5P	96.80	65.30	743

Literature-anchored findings (GeneRIF, showing 17)

• Enigma protein shown to interact with alpha actinin 2 by yeast two-hybrid screening and immunochemistry (co-localization at myocardial Z-disks). (PMID:10861853)
• CLP-36 contains a PDZ- and LIM domain, is widely expressed, interacts with actinin-1, actinin-2 and actinin-4, and localizes to actin stress fibers. The gene (7 exons) is localised to contig NT_008878.2 on chromosome 10. (PMID:11110697)
• results establish the CLP-36 PDZ-LIM protein as an adapter, recruiting the Clik1 kinase to actin stress fibers in nonmuscle cells, and suggest that Clik1 represents a novel regulator of actin stress fibers (PMID:11973348)
• We present evidence for the exclusive protein expression of CLP36 in proliferative and early post-proliferative trophoblast cells. (PMID:16609848)
• PDLIM1 showed moderate parent-of origin effects for some single nucleotide polymorphisms in attention deficit disorder with hyperactivity. (PMID:21651830)
• Alpha-actinin-4 and CLP36 protein deficiencies contribute to podocyte defects in multiple human glomerulopathies (PMID:21680739)
• Robust co-regulation of tyrosine phosphorylation sites has been revealed on novel protein interactions between EGFR and PDLIM1. (PMID:22851037)
• Femtomolar Zn2+ affinity of LIM domain of PDLIM1 protein uncovers crucial contribution of protein-protein interactions to protein stability. (PMID:22922308)
• Our results identify CLP36 as an important regulator of breast cancer cell migration and metastasis, and shed light on how increased CLP36 expression contributes to the progression of breast cancer. (PMID:24662836)
• PDLIM1 was shown to interact with p75(NTR) in highly invasive patient-derived glioma stem cells/tumor-initiating cells and shRNA knockdown of PDLIM1 in vitro and in vivo results in complete ablation of p75(NTR)-mediated invasion. (PMID:26119933)
• downregulation of PDLIM1 in colorectal cancer samples correlated with reduced E-cadherin and membrane beta-catenin levels (PMID:26701804)
• High titers of both TYMS and PDLIM1 serum autoantibodies were significantly more prevalent in breast cancer cases than in controls. (PMID:27068564)
• PDLIM1 Inhibits Tumor Metastasis Through Activating Hippo Signaling in Hepatocellular Carcinoma. (PMID:31509262)
• MicroRNA-370-3p inhibits cell proliferation and induces chronic myelogenous leukaemia cell apoptosis by suppressing PDLIM1/Wnt/beta-catenin signaling. (PMID:31986893)
• Distribution of PDLIM1 at actin-rich structures generated by invasive and adherent bacterial pathogens. (PMID:33022122)
• Hyperprogression on immunotherapy with complete response to chemotherapy in a NSCLC patient with high PD-L1 and STK11: A case report. (PMID:33181636)
• PDLIM1 interacts with HK2 to promote gastric cancer progression through enhancing the Warburg effect via Wnt/beta-catenin signaling. (PMID:37930472)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdlim1	ENSDARG00000019845
mus_musculus	Pdlim1	ENSMUSG00000055044
rattus_norvegicus	Pdlim1	ENSRNOG00000016166
drosophila_melanogaster	Zasp52	FBGN0265991
caenorhabditis_elegans		WBGENE00001132

Paralogs (7): PDLIM2 (ENSG00000120913), LDB3 (ENSG00000122367), PDLIM4 (ENSG00000131435), PDLIM3 (ENSG00000154553), PDLIM5 (ENSG00000163110), PDLIM7 (ENSG00000196923), PRICKLE4 (ENSG00000278224)

Protein

Protein identifiers

PDZ and LIM domain protein 1 — O00151 (reviewed: O00151)

Alternative names: C-terminal LIM domain protein 1, Elfin, LIM domain protein CLP-36

All UniProt accessions (2): O00151, V9HW92

UniProt curated annotations — full annotation on UniProt →

Function. Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton. Involved in assembly, disassembly and directioning of stress fibers in fibroblasts. Required for the localization of ACTN1 and PALLD to stress fibers. Required for cell migration and in maintaining cell polarity of fibroblasts.

Subunit / interactions. Interacts with ACTN1, ACTN2 and ACTN4. Interacts with PDLIM4.

Subcellular location. Cytoplasm. Cytoskeleton. Myofibril. Sarcomere. Z line.

Tissue specificity. Strongly expressed in the heart and skeletal muscle, moderately expressed in the spleen, small intestine, colon, placenta, and lung. A lower level expression is seen in liver, thymus, kidney, prostate and pancreas and is not found in the brain, testis, ovary, and peripheral blood leukocytes.

RefSeq proteins (1): NP_066272* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001478	PDZ	Domain
IPR001781	Znf_LIM	Domain
IPR006643	Zasp-like_motif	Domain
IPR028537	PDLIM1_LIM	Domain
IPR031847	PDLI1-4/Zasp-like_mid	Domain
IPR036034	PDZ_sf	Homologous_superfamily
IPR050604	PDZ-LIM_domain	Family

Pfam: PF00412, PF00595, PF15936

UniProt features (34 total): binding site 8, strand 8, modified residue 6, helix 5, domain 2, initiator methionine 1, chain 1, sequence variant 1, sequence conflict 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2PKT	X-RAY DIFFRACTION	1.5
1X62	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O00151-F1	70.57	0.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 307; 310; 260; 263; 280; 283; 286; 289

Post-translational modifications (6): 2, 90, 130, 144, 316, 321

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 376 (showing top): GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, CHUNG_BLISTER_CYTOTOXICITY_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, HSIAO_HOUSEKEEPING_GENES, HNF1_Q6, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, GOBP_CELL_CELL_ADHESION, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN, FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP, RICKMAN_METASTASIS_DN, ONKEN_UVEAL_MELANOMA_UP, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT

GO Biological Process (12): response to hypoxia (GO:0001666), regulation of transcription by RNA polymerase II (GO:0006357), response to oxidative stress (GO:0006979), heart development (GO:0007507), fibroblast migration (GO:0010761), maintenance of cell polarity (GO:0030011), actin cytoskeleton organization (GO:0030036), establishment or maintenance of actin cytoskeleton polarity (GO:0030950), stress fiber assembly (GO:0043149), muscle structure development (GO:0061061), positive regulation of DNA-templated transcription (GO:0045893), cell-cell adhesion (GO:0098609)

GO Molecular Function (6): transcription coactivator activity (GO:0003713), actin binding (GO:0003779), metal ion binding (GO:0046872), muscle alpha-actinin binding (GO:0051371), cadherin binding involved in cell-cell adhesion (GO:0098641), protein binding (GO:0005515)

GO Cellular Component (9): stress fiber (GO:0001725), transcription regulator complex (GO:0005667), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), adherens junction (GO:0005912), focal adhesion (GO:0005925), Z disc (GO:0030018), filamentous actin (GO:0031941), actin cytoskeleton (GO:0015629)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to stress	2
regulation of DNA-templated transcription	2
protein-containing complex	2
cellular anatomical structure	2
response to decreased oxygen levels	1
transcription by RNA polymerase II	1
animal organ development	1
circulatory system development	1
ameboidal-type cell migration	1
establishment or maintenance of cell polarity	1
cytoskeleton organization	1
actin filament-based process	1
actin cytoskeleton organization	1
establishment or maintenance of cytoskeleton polarity	1
contractile actin filament bundle assembly	1
actomyosin structure organization	1
anatomical structure development	1
DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
cell adhesion	1
transcription coregulator activity	1
positive regulation of DNA-templated transcription	1
cytoskeletal protein binding	1
cation binding	1
alpha-actinin binding	1
cadherin binding	1
cell-cell adhesion	1
cell-cell adhesion mediator activity	1
binding	1
actomyosin	1
contractile actin filament bundle	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
cell-cell junction	1
cell-substrate junction	1
I band	1
actin filament	1
cytoskeleton	1

Protein interactions and networks

STRING

1480 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDLIM1	STK35	Q8TDR2	941
PDLIM1	ACTN1	P12814	854
PDLIM1	ACTN4	O43707	821
PDLIM1	ACTN2	P35609	778
PDLIM1	GSN	P06396	636
PDLIM1	VCL	P18206	619
PDLIM1	ESR1	P03372	600
PDLIM1	A0A0A0MSP3	A0A0A0MSP3	534
PDLIM1	MYOT	Q9UBF9	523
PDLIM1	TPM4	P07226	505
PDLIM1	TPM2	P06468	501
PDLIM1	RSU1	Q15404	486
PDLIM1	SCIN	Q9Y6U3	475
PDLIM1	TGM2	P21980	468
PDLIM1	SDC4	P31431	437

IntAct

456 interactions, top by confidence:

A	B	Type	Score
PDLIM1	ACTN4	psi-mi:“MI:0914”(association)	0.800
ACTN4	PDLIM1	psi-mi:“MI:0915”(physical association)	0.800
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
ACTN2	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.690
PDLIM1	GFAP	psi-mi:“MI:0915”(physical association)	0.670
GFAP	PDLIM1	psi-mi:“MI:0915”(physical association)	0.670
CFTR	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.670
SOX2	PDLIM1	psi-mi:“MI:0914”(association)	0.530
IFNAR2	PDLIM1	psi-mi:“MI:0914”(association)	0.500
HORMAD2	PDLIM1	psi-mi:“MI:0915”(physical association)	0.500
IFNAR2	PDLIM1	psi-mi:“MI:0915”(physical association)	0.500
MAP1LC3C	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
PDLIM1	RPS6KA1	psi-mi:“MI:0407”(direct interaction)	0.440
PDLIM1	PALLD	psi-mi:“MI:0407”(direct interaction)	0.440
MYOZ3	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
MYPN	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
MYOZ2	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
MYOT	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
TJP3	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
LNX2	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
KCNA5	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
GAS2L2	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440
SLC15A5	PDLIM1	psi-mi:“MI:0407”(direct interaction)	0.440

BioGRID (153): PDLIM1 (Affinity Capture-RNA), PDLIM1 (Affinity Capture-MS), PDLIM1 (Affinity Capture-MS), ACTN4 (Affinity Capture-MS), ACTN1 (Affinity Capture-MS), ACTN2 (Affinity Capture-MS), ACTN3 (Affinity Capture-MS), NUDT12 (Affinity Capture-MS), RANGRF (Affinity Capture-MS), PDLIM1 (Two-hybrid), PDLIM1 (Two-hybrid), PDLIM1 (Two-hybrid), PDLIM1 (Co-fractionation), STMN1 (Co-fractionation), PDLIM1 (Affinity Capture-MS)

ESM2 similar proteins: A0M8R4, A0M8S5, A0M8U6, A8K855, O00151, P47226, P52944, P60670, Q00PK1, Q07DW1, Q07DX3, Q07DY3, Q07DZ4, Q07E27, Q07E40, Q07E51, Q09YI0, Q09YJ2, Q09YK3, Q09YL5, Q09YN8, Q0E908, Q108U9, Q17QE2, Q2IBA3, Q2IBC3, Q2IBH0, Q2LAP6, Q2QL92, Q2QLA1, Q2QLB2, Q2QLC3, Q2QLE3, Q2QLF4, Q2QLG8, Q2QLH9, Q2YDE9, Q5PXT2, Q5RC52, Q6DIR5

Diamond homologs: A1ZA47, A2ALU4, A5H447, D4A702, E1BKA3, O00151, O14639, O43294, O60711, O70209, O70400, O75112, O94929, P20271, P48059, P49023, P49024, P50464, P52944, Q09476, Q0WSN2, Q13796, Q15942, Q1JQB5, Q2KJ33, Q2TCH4, Q2YDK0, Q3MHZ4, Q3SX26, Q3SX40, Q3SYZ8, Q3T0X8, Q3TJD7, Q55BI0, Q5F464, Q5R7I1, Q5RCF7, Q5TD97, Q5U2Z2, Q5XI07

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 189 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
RHOQ GTPase cycle	7	10.6×	5e-04
Transcriptional and post-translational regulation of MITF-M expression and activity	6	8.9×	4e-03
CDC42 GTPase cycle	10	6.0×	6e-04
RHO GTPase cycle	12	6.0×	5e-04
RAC1 GTPase cycle	11	5.6×	5e-04
RHOA GTPase cycle	9	5.6×	3e-03
Signaling by Rho GTPases	15	4.3×	5e-04
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	15	4.2×	5e-04

GO biological processes:

GO term	Partners	Fold	FDR
cell-cell adhesion	11	6.5×	6e-04
cell migration	14	5.0×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

821 predictions. Top by Δscore:

Variant	Effect	Δscore
10:95238107:CACCA:C	acceptor_gain	1.0000
10:95238109:CCA:C	acceptor_gain	1.0000
10:95238110:CA:C	acceptor_gain	1.0000
10:95238110:CAC:C	acceptor_gain	1.0000
10:95238112:C:CC	acceptor_gain	1.0000
10:95238561:TAC:T	donor_loss	1.0000
10:95238562:AC:A	donor_loss	1.0000
10:95238563:C:CG	donor_loss	1.0000
10:95238565:CACAC:C	donor_loss	1.0000
10:95238566:A:AC	donor_gain	1.0000
10:95238566:A:C	donor_loss	1.0000
10:95238567:C:CA	donor_gain	1.0000
10:95238567:CA:C	donor_gain	1.0000
10:95238567:CACA:C	donor_gain	1.0000
10:95238605:T:TA	donor_gain	1.0000
10:95238682:TCCC:T	acceptor_gain	1.0000
10:95238683:CCC:C	acceptor_gain	1.0000
10:95238683:CCCC:C	acceptor_gain	1.0000
10:95238684:CC:C	acceptor_gain	1.0000
10:95238684:CCC:C	acceptor_gain	1.0000
10:95238685:CC:C	acceptor_gain	1.0000
10:95238686:C:CC	acceptor_gain	1.0000
10:95238687:T:G	acceptor_loss	1.0000
10:95247367:C:CC	acceptor_gain	1.0000
10:95263862:A:AC	donor_gain	1.0000
10:95263863:C:CG	donor_gain	1.0000
10:95263863:CGG:C	donor_gain	1.0000
10:95263863:CGGT:C	donor_gain	1.0000
10:95268773:CTTA:C	donor_loss	1.0000
10:95268774:TTA:T	donor_loss	1.0000

AlphaMissense

2165 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:95237983:G:T	A311D	1.000
10:95237995:C:T	C307Y	1.000
10:95237996:A:G	C307R	1.000
10:95238018:G:C	F299L	1.000
10:95238018:G:T	F299L	1.000
10:95238020:A:G	F299L	1.000
10:95238057:G:C	C286W	1.000
10:95238058:C:G	C286S	1.000
10:95238058:C:T	C286Y	1.000
10:95238059:A:G	C286R	1.000
10:95238059:A:T	C286S	1.000
10:95238593:A:G	C260R	1.000
10:95247244:A:G	L219S	1.000
10:95247252:G:C	F216L	1.000
10:95247252:G:T	F216L	1.000
10:95247253:A:C	F216C	1.000
10:95247253:A:G	F216S	1.000
10:95247254:A:G	F216L	1.000
10:95271685:C:G	A66P	1.000
10:95290833:A:T	L28H	1.000
10:95290854:C:T	G21D	1.000
10:95290855:C:G	G21R	1.000
10:95290857:C:A	G20V	1.000
10:95290857:C:T	G20D	1.000
10:95290858:C:A	G20C	1.000
10:95290858:C:G	G20R	1.000
10:95290869:A:G	F16S	1.000
10:95290873:C:G	G15R	1.000
10:95237994:A:C	C307W	0.999
10:95237995:C:A	C307F	0.999

dbSNP variants (sampled 300 via entrez): RS1000035864 (10:95271695 T>C,G), RS1000083911 (10:95281062 C>T), RS1000268790 (10:95246991 G>C,T), RS1000339445 (10:95261283 T>C), RS1000359280 (10:95241049 G>A), RS1000394429 (10:95267990 G>A), RS1000448215 (10:95245690 A>C), RS1000469556 (10:95265650 C>A), RS1000500292 (10:95245931 T>A), RS1000511867 (10:95237128 G>A), RS1000522317 (10:95254919 T>C), RS1000593593 (10:95291965 C>T), RS1000685692 (10:95248175 C>T), RS1000731226 (10:95284510 C>G,T), RS1000772641 (10:95261655 T>G)

Disease associations

OMIM: gene MIM:605900 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST000854_3	Suicide risk	3.000000e-06
GCST004599_7	Mean platelet volume	3.000000e-14
GCST90002384_272	Hemoglobin	3.000000e-10
GCST90002395_30	Mean platelet volume	8.000000e-23
GCST90002407_309	White blood cell count	6.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004321	attempted suicide
EFO:0004509	hemoglobin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	7
bisphenol A	decreases methylation, decreases expression, increases expression, affects cotreatment	4
Tobacco Smoke Pollution	decreases expression, affects expression	4
methylmercuric chloride	decreases expression, increases expression, affects cotreatment	3
trichostatin A	affects cotreatment, increases expression	3
Cisplatin	affects expression, affects cotreatment, increases expression	3
bisphenol F	increases expression, affects cotreatment	2
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment, decreases expression	2
belinostat	increases expression, affects cotreatment	2
bisphenol S	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Aerosols	increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Dexamethasone	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Progesterone	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
Particulate Matter	affects expression, increases reaction, increases expression	2
aristolochic acid I	decreases expression	1
chloroacetaldehyde	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression, increases expression	1
sulforaphane	decreases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
coumarin	increases phosphorylation	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A5G5	SEES3-1V human PDLIM1, clone1	Embryonic stem cell	Male
CVCL_A5G6	SEES3-1V human PDLIM1, clone2	Embryonic stem cell	Male
CVCL_A5G7	SEES3-1V human PDLIM1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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