Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	11155
Gene name	LIM domain binding 3
Gene symbol	LDB3
Synonyms (NCBI Gene)	CMD1CCMD2LCMH24CMPD3CYPHERLDB3Z1LDB3Z4LVNC3MFM4ORACLEPDLIM6ZASP
Chromosome	10
Chromosome location	10q23.2
Summary	This gene encodes a PDZ domain-containing protein. PDZ motifs are modular protein-protein interaction domains consisting of 80-120 amino acid residues. PDZ domain-containing proteins interact with each other in cytoskeletal assembly or with other proteins

Show/Hide all (27)

SNP ID	Visualize variation	Clinical significance	Consequence
rs45458895	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs45487699	C>G,T	Conflicting-interpretations-of-pathogenicity, pathogenic, uncertain-significance	Intron variant, coding sequence variant, missense variant
rs45514002	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, genic downstream transcript variant
rs77304928	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant
rs121908333	G>A	Pathogenic, uncertain-significance	Intron variant, missense variant, coding sequence variant
rs121908334	C>T	Pathogenic, uncertain-significance	Intron variant, missense variant, coding sequence variant
rs121908335	C>T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs121908336	C>G,T	Benign-likely-benign, pathogenic, likely-benign	Genic downstream transcript variant, intron variant, synonymous variant, missense variant, coding sequence variant
rs121908337	C>T	Pathogenic	Missense variant, coding sequence variant, intron variant
rs121908339	A>T	Pathogenic, uncertain-significance	Intron variant, missense variant, coding sequence variant
rs138251566	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Genic downstream transcript variant, missense variant, coding sequence variant, intron variant
rs138951890	A>C,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Genic downstream transcript variant, missense variant, coding sequence variant
rs139922045	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs143764931	G>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Genic downstream transcript variant, missense variant, coding sequence variant
rs144445130	G>A	Conflicting-interpretations-of-pathogenicity, benign, likely-benign	Synonymous variant, coding sequence variant, intron variant
rs145983824	C>T	Uncertain-significance, pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs200796750	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, genic downstream transcript variant, missense variant, intron variant
rs201968775	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, intron variant, missense variant
rs281865143	C>T	Uncertain-significance, pathogenic	Coding sequence variant, intron variant, missense variant
rs374613600	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs397517209	CCCTGCCCCTGCCTACACCCCCTCCCCTGCCCCTGCCTACACCCCCTC>-,CCCTGCCCCTGCCTACACCCCCTC,CCCTGCCCCTGCCTACACCCCCTCCCCTGCCCCTGCCTACACCCCCTCCCCTGCCCCTGCCTACACCCCCTC	Conflicting-interpretations-of-pathogenicity, uncertain-significance, benign	Coding sequence variant, inframe deletion, genic downstream transcript variant, inframe insertion
rs727503126	C>G,T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs727503129	C>-	Uncertain-significance, likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs747523570	G>A,C	Uncertain-significance, likely-pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs774886148	A>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, intron variant, missense variant
rs775180716	C>T	Pathogenic	Coding sequence variant, missense variant
rs1131691665	G>T	Likely-pathogenic	Intron variant, coding sequence variant, missense variant

Show/Hide all (83)

miRTarBase ID	miRNA	Experiments
MIRT1106253	hsa-miR-122	CLIP-seq
MIRT1106254	hsa-miR-1292	CLIP-seq
MIRT1106255	hsa-miR-129-5p	CLIP-seq
MIRT1106256	hsa-miR-3135b	CLIP-seq
MIRT1106257	hsa-miR-3150b-3p	CLIP-seq
MIRT1106258	hsa-miR-3652	CLIP-seq
MIRT1106259	hsa-miR-3667-3p	CLIP-seq
MIRT1106260	hsa-miR-4423-5p	CLIP-seq
MIRT1106261	hsa-miR-4430	CLIP-seq
MIRT1106262	hsa-miR-450b-5p	CLIP-seq
MIRT1106263	hsa-miR-4689	CLIP-seq
MIRT1106264	hsa-miR-4784	CLIP-seq
MIRT1106265	hsa-miR-507	CLIP-seq
MIRT1106266	hsa-miR-557	CLIP-seq
MIRT1106267	hsa-miR-891a	CLIP-seq
MIRT1106268	hsa-miR-3616-3p	CLIP-seq
MIRT1106269	hsa-miR-4419a	CLIP-seq
MIRT1106270	hsa-miR-4436b-3p	CLIP-seq
MIRT1106271	hsa-miR-4510	CLIP-seq
MIRT1106272	hsa-miR-520a-5p	CLIP-seq
MIRT1106273	hsa-miR-525-5p	CLIP-seq
MIRT1106274	hsa-miR-885-3p	CLIP-seq
MIRT1106275	hsa-miR-1228	CLIP-seq
MIRT1106276	hsa-miR-4715-3p	CLIP-seq
MIRT1106277	hsa-miR-4722-3p	CLIP-seq
MIRT1106278	hsa-miR-4735-5p	CLIP-seq
MIRT1106279	hsa-miR-4763-5p	CLIP-seq
MIRT1106280	hsa-miR-4775	CLIP-seq
MIRT1106281	hsa-miR-4794	CLIP-seq
MIRT1106282	hsa-miR-566	CLIP-seq
MIRT1106283	hsa-miR-590-3p	CLIP-seq
MIRT1106255	hsa-miR-129-5p	CLIP-seq
MIRT1106262	hsa-miR-450b-5p	CLIP-seq
MIRT1106265	hsa-miR-507	CLIP-seq
MIRT1106266	hsa-miR-557	CLIP-seq
MIRT1106267	hsa-miR-891a	CLIP-seq
MIRT1106255	hsa-miR-129-5p	CLIP-seq
MIRT1106262	hsa-miR-450b-5p	CLIP-seq
MIRT1106280	hsa-miR-4775	CLIP-seq
MIRT1106265	hsa-miR-507	CLIP-seq
MIRT1106266	hsa-miR-557	CLIP-seq
MIRT1106283	hsa-miR-590-3p	CLIP-seq
MIRT1106267	hsa-miR-891a	CLIP-seq
MIRT2029400	hsa-miR-1202	CLIP-seq
MIRT2029401	hsa-miR-15a	CLIP-seq
MIRT2029402	hsa-miR-15b	CLIP-seq
MIRT2029403	hsa-miR-16	CLIP-seq
MIRT2029404	hsa-miR-195	CLIP-seq
MIRT2029405	hsa-miR-214	CLIP-seq
MIRT2029406	hsa-miR-216a	CLIP-seq
MIRT2029407	hsa-miR-216b	CLIP-seq
MIRT2029408	hsa-miR-3194-5p	CLIP-seq
MIRT2029409	hsa-miR-3619-5p	CLIP-seq
MIRT2029410	hsa-miR-3972	CLIP-seq
MIRT2029411	hsa-miR-424	CLIP-seq
MIRT1106260	hsa-miR-4423-5p	CLIP-seq
MIRT2029412	hsa-miR-4530	CLIP-seq
MIRT2029413	hsa-miR-4660	CLIP-seq
MIRT2029414	hsa-miR-4722-5p	CLIP-seq
MIRT1106279	hsa-miR-4763-5p	CLIP-seq
MIRT2029415	hsa-miR-497	CLIP-seq
MIRT2029416	hsa-miR-646	CLIP-seq
MIRT2029417	hsa-miR-761	CLIP-seq
MIRT2029400	hsa-miR-1202	CLIP-seq
MIRT2029410	hsa-miR-3972	CLIP-seq
MIRT1106275	hsa-miR-1228	CLIP-seq
MIRT1106276	hsa-miR-4715-3p	CLIP-seq
MIRT1106277	hsa-miR-4722-3p	CLIP-seq
MIRT1106278	hsa-miR-4735-5p	CLIP-seq
MIRT1106279	hsa-miR-4763-5p	CLIP-seq
MIRT1106281	hsa-miR-4794	CLIP-seq
MIRT1106282	hsa-miR-566	CLIP-seq
MIRT1106275	hsa-miR-1228	CLIP-seq
MIRT2683841	hsa-miR-2113	CLIP-seq
MIRT1106276	hsa-miR-4715-3p	CLIP-seq
MIRT1106277	hsa-miR-4722-3p	CLIP-seq
MIRT1106278	hsa-miR-4735-5p	CLIP-seq
MIRT1106279	hsa-miR-4763-5p	CLIP-seq
MIRT1106280	hsa-miR-4775	CLIP-seq
MIRT1106281	hsa-miR-4794	CLIP-seq
MIRT1106282	hsa-miR-566	CLIP-seq
MIRT1106283	hsa-miR-590-3p	CLIP-seq
MIRT2683842	hsa-miR-599	CLIP-seq

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001725	Component	Stress fiber	IBA
GO:0003779	Function	Actin binding	IBA
GO:0005080	Function	Protein kinase C binding	IEA
GO:0005515	Function	Protein binding	IPI	10427098
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IDA	10427098
GO:0005856	Component	Cytoskeleton	IEA
GO:0005912	Component	Adherens junction	IBA
GO:0007507	Process	Heart development	IBA
GO:0008092	Function	Cytoskeletal protein binding	IPI	17987659
GO:0019899	Function	Enzyme binding	IEA
GO:0030018	Component	Z disc	IBA
GO:0030018	Component	Z disc	IDA	10427098
GO:0030018	Component	Z disc	IEA
GO:0030036	Process	Actin cytoskeleton organization	IBA
GO:0031143	Component	Pseudopodium	IEA
GO:0031941	Component	Filamentous actin	IBA
GO:0042995	Component	Cell projection	IEA
GO:0045214	Process	Sarcomere organization	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0051371	Function	Muscle alpha-actinin binding	IBA
GO:0051371	Function	Muscle alpha-actinin binding	IEA
GO:0061061	Process	Muscle structure development	IBA

MIM	HGNC	e!Ensembl
605906	15710	ENSG00000122367

O75112

Protein name

LIM domain-binding protein 3 (Protein cypher) (Z-band alternatively spliced PDZ-motif protein)

Protein function

May function as an adapter in striated muscle to couple protein kinase C-mediated signaling via its LIM domains to the cytoskeleton.

PDB

1RGW , 4YDP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00595	PDZ	3 → 81	PDZ domain	Domain
PF15936	DUF4749	192 → 297	Domain of unknown function (DUF4749)	Family
PF00412	LIM	551 → 606	LIM domain	Domain
PF00412	LIM	610 → 665	LIM domain	Domain
PF00412	LIM	669 → 725	LIM domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed primarily in skeletal muscle and to a lesser extent in heart. Also detected in brain and placenta. {ECO:0000269|PubMed:10427098}.

Sequence

MSYSVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTM
THLEAQNKIKSASYNLSLTLQKSKRPIPISTTAPPVQTPLPVIPHQKDPALDTNGSLVAP
SPSPEARASPGTPGTPELRPTFSPAFSRPSAFSSLAEASDPGPPRASLRAKTSPEGARDL
LGPKALPGSSQPRQYNNPIGLYSAETLREMAQMYQMSLRGKASGVGLPGGSLPIKDLAVD
SASPVYQAVIKSQNKPEDEADEWARRSSNLQSRSFRILAQMTGTEFMQDPDEEALRRSST
PIEHAPVCTSQATTPLLPASAQPPAAASPSAASPPLATAAAHTAIASASTTAPASSPADS
PRPQASSYSPAVAASSAPATHTSYSEGPAAPAPKPRVVTTASIRPSVYQPVPASTYSPSP
GANYSPTPYTPSPAPAYTPSPAPAYTPSPVPTYTPSPAPAYTPSPAPNYNPAPSVAYSGG
PAEPASRPPWVTDDSFSQKFAPGKSTTSISKQTLPRGGPAYTPAGPQVPPLARGTVQRAE
RFPASSRTPLCGHCNNVIRGPFLVAMGRSWHPEEFTCAYCKTSLADVCFVEEQNNVYCER
CYEQFFAPLCAKCNTKIMGEVMHALRQTWHTTCFVCAACKKPFGNSLFHMEDGEPYCEKD
YINLFSTKCHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDRPLCKK
HAHTINL

Sequence length

727

Interactions

View interactions

	KEGG
	Cytoskeleton in muscle cells

2060

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cardiomyopathy	Likely pathogenic; Pathogenic	rs121908333, rs121908334	RCV000770149 RCV000769278
Cardiovascular phenotype	Likely pathogenic; Pathogenic	rs121908334	RCV003162208
Dilated cardiomyopathy 1C	Likely pathogenic; Pathogenic	rs121908333, rs121908334, rs959113234, rs1846937833, rs1846942383	RCV003483424 RCV002247249 RCV001293337 RCV001293342 RCV001293343
LDB3-related disorder	Likely pathogenic; Pathogenic	rs121908334	RCV003934799
Myofibrillar myopathy	Likely pathogenic; Pathogenic	rs121908334	RCV000239669
Myofibrillar myopathy 4	Pathogenic; Likely pathogenic	rs2132363967, rs2132482311, rs2132485699, rs2132363722, rs45581435, rs2132487443, rs121908333, rs121908334, rs2492677971, rs2492762089, rs2492808478, rs45487699, rs1308589918, rs1060501315, rs730880345 View all (5 more)	RCV001367317 RCV001924262 RCV002017623 RCV001948424 RCV001948664 RCV001969481 RCV000004992 RCV000004993 RCV002867919 RCV003503538 RCV003502930 RCV003504114 RCV003504502 RCV000459772 RCV000559443 RCV000639863 RCV000639874 RCV000639870 RCV003611875 RCV001248403
Neuromuscular disease	Likely pathogenic; Pathogenic	rs121908334	RCV000036847

Show/Hide Unknown Diseases (27)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Arrhythmogenic right ventricular cardiomyopathy	Conflicting classifications of pathogenicity	rs372331627	RCV000852622
Cardiomyopathy, dilated, 2l	Conflicting classifications of pathogenicity	rs1308589918, rs2492777637, rs779919472	RCV005419167 RCV005419445 RCV005418368
Dilated cardiomyopathy 1A	Conflicting classifications of pathogenicity	rs45487699, rs139104492, rs138251566	RCV001256801 RCV001256802 RCV001256803
Dilated Cardiomyopathy, Dominant	Conflicting classifications of pathogenicity; Uncertain significance; Likely benign; Benign	rs371708921, rs754704023, rs764620834, rs139415121, rs754174632, rs532856980, rs886047355, rs34972863, rs761090088, rs185972751, rs549156118, rs45592139, rs45529531, rs34423165, rs76615432, rs71473272, rs3740343 View all (2 more)	RCV000389071 RCV000267983 RCV000319187 RCV000380800 RCV000379731 RCV000292468 RCV000323243 RCV000353070 RCV000364330 RCV000303374 RCV000335474 RCV000396844 RCV000288174 RCV000259558 RCV000334935 RCV000343074 RCV000303793 RCV000382414
Familial hypertrophic cardiomyopathy 24	Conflicting classifications of pathogenicity; Uncertain significance	rs45487699, rs145983824	RCV000170300 RCV000170304
Familial isolated dilated cardiomyopathy	Conflicting classifications of pathogenicity; Uncertain significance	rs143764931, rs1370639524	RCV002470802 RCV002470983
Gastric cancer	Benign; Likely benign	rs140347820	RCV005890023
Hypertrophic cardiomyopathy	Uncertain significance; Conflicting classifications of pathogenicity	rs367792378, rs200796750, rs138251566, rs397517226, rs779919472	RCV000497637 RCV001254737 RCV000853422 RCV000991353 RCV000852433
Hypertrophic cardiomyopathy 1	Uncertain significance	rs762580653	RCV000201919
Hypertrophic cardiomyopathy 14	Uncertain significance	rs1135401943	RCV000496503
Hypertrophic cardiomyopathy 2	Benign; Likely benign	rs868594949, rs1009984915, rs761685061, rs769720685	RCV004596480 RCV004596486 RCV004596411 RCV004596412
Hypertrophic cardiomyopathy 4	Uncertain significance	rs777364128	RCV004546858
Isolated Noncompaction of the Ventricular Myocardium	Uncertain significance	rs1589674758	RCV001375639
Left ventricular noncompaction 1	Uncertain significance	rs915830221, rs1846876959	RCV000626096 RCV001256800
Left ventricular noncompaction 3	Conflicting classifications of pathogenicity	rs45514002	RCV000005001
Left ventricular noncompaction cardiomyopathy	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs2803558, rs371708921, rs200596619, rs754704023, rs766817285, rs764620834, rs139415121, rs754174632, rs200580597, rs886047356, rs45578532, rs886047354, rs34972863, rs761090088, rs185972751 View all (8 more)	RCV000393181 RCV000332141 RCV000157287 RCV000301609 RCV000322185 RCV000279363 RCV000291069 RCV000287151 RCV000367463 RCV000402977 RCV000319249 RCV000320704 RCV000322842 RCV000276729 RCV000297716 RCV000275628 RCV000389822 RCV000338341 RCV000347861 RCV000354520 RCV000380869 RCV000374491 RCV000365510 RCV000853181
Long QT syndrome	Uncertain significance; Likely benign	rs369419493, rs397517216, rs181700296, rs1589675054	RCV003318402 RCV003318448 RCV000852619 RCV003318387
Lung cancer	Benign; Likely benign	rs45579241, rs140347820	RCV005890021 RCV005890024
Malignant tumor of urinary bladder	Benign; Likely benign	rs140347820	RCV005890022
Myofibrillar Myopathy, Dominant	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs2803558, rs371708921, rs754704023, rs766817285, rs764620834, rs139415121, rs754174632, rs200580597, rs532856980, rs886047355, rs886047356, rs45578532, rs886047354, rs34972863, rs761090088 View all (10 more)	RCV000393189 RCV000292985 RCV000360274 RCV000283535 RCV000261573 RCV000346037 RCV000342117 RCV000393350 RCV000404259 RCV000268153 RCV000371418 RCV000261647 RCV000265698 RCV000379799 RCV000334179 RCV000357141 RCV000329332 RCV000295608 RCV000396879 RCV000393351 RCV000319367 RCV000271123 RCV000282359 RCV000395286 RCV000307366 RCV000295142
Ovarian serous cystadenocarcinoma	Benign	rs59439194	RCV005903950
Primary dilated cardiomyopathy	Conflicting classifications of pathogenicity; Uncertain significance; Benign; Likely benign	rs121908338, rs367792378, rs45458895, rs769156627, rs376489385, rs146265188	RCV000172755 RCV001375638 RCV001375640 RCV001090046 RCV000853126 RCV000852621
Primary familial dilated cardiomyopathy	Conflicting classifications of pathogenicity; Uncertain significance	rs121908335, rs149348427, rs755513516, rs141870580, rs138951890, rs775232208	RCV000845475 RCV000845500 RCV000623559 RCV000622484 RCV000623075 RCV000845315
Primary familial hypertrophic cardiomyopathy	Uncertain significance; Conflicting classifications of pathogenicity	rs587782955, rs730880127, rs730880128, rs730880129, rs147072071, rs61857115, rs1261515174, rs1589676793, rs745444678, rs1354084230	RCV000143909 RCV000157286 RCV000157288 RCV000157289 RCV000845399 RCV000208404 RCV000853154 RCV000853175 RCV000853155 RCV005419050
Sarcoma	Benign	rs59439194	RCV005903949
Uterine carcinosarcoma	Benign	rs45579241, rs59439194	RCV005890020 RCV005903951
Ventricular tachycardia	Likely benign	rs1589674796	RCV000852620

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Arrhythmias Cardiac	Associate	33949037
Barth Syndrome	Associate	17394203
Cardiomyopathy Dilated	Associate	14662268, 17394203, 20201937, 31024045, 31379146, 33949037
Cardiomyopathy Hypertrophic	Associate	21896538, 32344918
Deafness	Associate	26636822
Death Sudden Cardiac	Associate	33949037
familial dilated cardiomyopathy	Associate	19412328
Fibrosis	Associate	27135274
Heart Diseases	Associate	26419279, 26636822, 31379146, 36721086
Heart Septal Defects Ventricular	Associate	26419279
Isolated Noncompaction of the Ventricular Myocardium	Associate	14662268, 17394203
Multiple Pterygium Syndrome Autosomal Dominant	Associate	17394203
Myocardial Stunning	Associate	26419279
Myopathy Central Core	Associate	26636822
Myotonic Dystrophy	Associate	20066428, 34371182
Pathological Conditions Anatomical	Associate	28821295
Prostatic Neoplasms	Associate	37960876
Squamous Cell Carcinoma of Head and Neck	Associate	35132271
Sudden Unexpected Death in Epilepsy	Associate	27135274
Tachycardia Sinus	Associate	28821295
Vacuolar myopathy	Associate	32419263
Ventricular Dysfunction Left	Associate	14662268, 28821295
Ventricular Fibrillation	Associate	33949037
Ventricular Remodeling	Associate	26419279, 27135274

LDB3 (LIM domain binding 3)