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	4054
Gene name	Latent transforming growth factor beta binding protein 3
Gene symbol	LTBP3
Synonyms (NCBI Gene)	DASSGPHYSD3LTBP-3LTBP2STHAG6pp6425
Chromosome	11
Chromosome location	11q13.1
Summary	The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also

Show/Hide all (13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121909145	G>A,C	Pathogenic	Coding sequence variant, stop gained, synonymous variant, non coding transcript variant
rs145001056	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs752375653	C>-,CC	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs796052116	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs875989822	TTTGAGCCGGTAGC>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs875989823	C>A	Pathogenic	Splice donor variant
rs875989824	C>-	Pathogenic	Frameshift variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs878853036	G>A	Pathogenic	Stop gained, genic downstream transcript variant, non coding transcript variant, coding sequence variant, intron variant
rs878853262	->C	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1064794603	GC>AG	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1188540819	C>T	Pathogenic	Intron variant
rs1286042594	C>-	Pathogenic	Non coding transcript variant, frameshift variant, 5 prime UTR variant, coding sequence variant
rs1554973844	C>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained

Show/Hide all (39)

miRTarBase ID	miRNA	Experiments	Reference
MIRT045534	hsa-miR-149-5p	CLASH	23622248
MIRT045534	hsa-miR-149-5p	CLASH	23622248
MIRT040731	hsa-miR-92b-3p	CLASH	23622248
MIRT035867	hsa-miR-1249-3p	CLASH	23622248
MIRT1122172	hsa-miR-1276	CLIP-seq
MIRT1122173	hsa-miR-3622a-5p	CLIP-seq
MIRT1122174	hsa-miR-4311	CLIP-seq
MIRT1122175	hsa-miR-583	CLIP-seq
MIRT2390394	hsa-miR-4728-5p	CLIP-seq
MIRT2465593	hsa-miR-1291	CLIP-seq
MIRT2465594	hsa-miR-328	CLIP-seq
MIRT2465595	hsa-miR-4707-3p	CLIP-seq
MIRT2465596	hsa-miR-4758-3p	CLIP-seq
MIRT2465597	hsa-miR-604	CLIP-seq
MIRT2465598	hsa-miR-658	CLIP-seq
MIRT2465599	hsa-miR-663b	CLIP-seq
MIRT2564059	hsa-miR-1225-3p	CLIP-seq
MIRT2564060	hsa-miR-1233	CLIP-seq
MIRT2465593	hsa-miR-1291	CLIP-seq
MIRT2564061	hsa-miR-3171	CLIP-seq
MIRT2465594	hsa-miR-328	CLIP-seq
MIRT2564062	hsa-miR-3607-5p	CLIP-seq
MIRT2465595	hsa-miR-4707-3p	CLIP-seq
MIRT2465596	hsa-miR-4758-3p	CLIP-seq
MIRT2465597	hsa-miR-604	CLIP-seq
MIRT2465598	hsa-miR-658	CLIP-seq
MIRT2465599	hsa-miR-663b	CLIP-seq
MIRT2564059	hsa-miR-1225-3p	CLIP-seq
MIRT2564060	hsa-miR-1233	CLIP-seq
MIRT2465593	hsa-miR-1291	CLIP-seq
MIRT2564061	hsa-miR-3171	CLIP-seq
MIRT2465594	hsa-miR-328	CLIP-seq
MIRT2564062	hsa-miR-3607-5p	CLIP-seq
MIRT2684284	hsa-miR-3940-3p	CLIP-seq
MIRT2465595	hsa-miR-4707-3p	CLIP-seq
MIRT2465596	hsa-miR-4758-3p	CLIP-seq
MIRT2465597	hsa-miR-604	CLIP-seq
MIRT2465598	hsa-miR-658	CLIP-seq
MIRT2465599	hsa-miR-663b	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	IEA
GO:0002062	Process	Chondrocyte differentiation	IEA
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	27339457
GO:0005576	Component	Extracellular region	HDA	27068509
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0007179	Process	Transforming growth factor beta receptor signaling pathway	IEA
GO:0007179	Process	Transforming growth factor beta receptor signaling pathway	IEA
GO:0007179	Process	Transforming growth factor beta receptor signaling pathway	IMP	18672106
GO:0019838	Function	Growth factor binding	IEA
GO:0030282	Process	Bone mineralization	IEA
GO:0030502	Process	Negative regulation of bone mineralization	IEA
GO:0031012	Component	Extracellular matrix	IDA	16157329
GO:0032331	Process	Negative regulation of chondrocyte differentiation	IEA
GO:0045595	Process	Regulation of cell differentiation	IEA
GO:0045780	Process	Positive regulation of bone resorption	IEA
GO:0046849	Process	Bone remodeling	IEA
GO:0050431	Function	Transforming growth factor beta binding	IEA
GO:0050431	Function	Transforming growth factor beta binding	IPI	10930463, 18672106
GO:0060349	Process	Bone morphogenesis	IEA
GO:0060430	Process	Lung saccule development	IEA
GO:0070062	Component	Extracellular exosome	HDA	19199708
GO:1902462	Process	Positive regulation of mesenchymal stem cell proliferation	IMP	18672106
GO:2000741	Process	Positive regulation of mesenchymal stem cell differentiation	IMP	18672106

MIM	HGNC	e!Ensembl
602090	6716	ENSG00000168056

Q9NS15

Protein name

Latent-transforming growth factor beta-binding protein 3 (LTBP-3)

Protein function

Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space. Associates specifically via disulfide bonds with the Latency-a

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00683	TB	289 → 327	TB domain	Family
PF07645	EGF_CA	355 → 394	Calcium-binding EGF domain	Domain
PF00683	TB	414 → 458	TB domain	Family
PF12662	cEGF	596 → 619	Complement Clr-like EGF-like	Domain
PF07645	EGF_CA	660 → 701	Calcium-binding EGF domain	Domain
PF07645	EGF_CA	703 → 742	Calcium-binding EGF domain	Domain
PF12662	cEGF	765 → 788	Complement Clr-like EGF-like	Domain
PF12661	hEGF	795 → 815	Human growth factor-like EGF	Domain
PF12662	cEGF	847 → 869	Complement Clr-like EGF-like	Domain
PF12661	hEGF	877 → 898	Human growth factor-like EGF	Domain
PF00683	TB	928 → 974	TB domain	Family
PF07645	EGF_CA	993 → 1034	Calcium-binding EGF domain	Domain
PF07645	EGF_CA	1036 → 1075	Calcium-binding EGF domain	Domain
PF07645	EGF_CA	1082 → 1121	Calcium-binding EGF domain	Domain
PF00683	TB	1147 → 1189	TB domain	Family
PF07645	EGF_CA	1254 → 1297	Calcium-binding EGF domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Isoform 2: Expressed prominently in heart, skeletal muscle, prostate, testis, small intestine and ovary (PubMed:12154076). Isoform 1: Strongly expressed in pancreas and liver (PubMed:12154076). {ECO:0000269|PubMed:12154076}.

Sequence

MPGPRGAAGGLAPEMRGAGAAGLLALLLLLLLLLLGLGGRVEGGPAGERGAGGGGALARE
RFKVVFAPVICKRTCLKGQCRDSCQQGSNMTLIGENGHSTDTLTGSGFRVVVCPLPCMNG
GQCSSRNQCLCPPDFTGRFCQVPAGGAGGGTGGSGPGLSRTGALSTGALPPLAPEGDSVA
SKHAIYAVQVIADPPGPGEGPPAQHAAFLVPLGPGQISAEVQAPPPVVNVRVHHPPEASV
QVHRIESSNAESAAPSQHLLPHPKPSHPRPPTQKPLGRCFQDTLPKQPCGSNPLPGLTKQ
EDCCGSIGTAWGQSKCHKCPQLQYTGVQKPGPVRGEVGADCPQGYKRLNSTHCQDINECA
MPGVCRHGDCLNNPGSYRCVCPPGHSLGPSRTQCIADKPEEKSLCFRLVSPEHQCQHPLT
TRLTRQLCCCSVGKAWGARCQRCPTDGTAAFKEICPAGKGYHILTSHQTLTIQGESDFSL
FLHPDGPPKPQQLPESPSQAPPPEDTEEERGVTTDSPVSEERSVQQSHPTATTTPARPYP
ELISRPSPPTMRWFLPDLPPSRSAVEIAPTQVTETDECRLNQNICGHGECVPGPPDYSCH
CNPGYRSHPQHRYCVDVNECEAEPCGPGRGICMNTGGSYNCHCNRGYRLHVGAGGRSCVD
LNECAKPHLCGDGGFCINFPGHYKCNCYPGYRLKASRPPVCEDIDECRDPSSCPDGKCEN
KPGSFKCIACQPGYRSQGGGACRDVNECAEGSPCSPGWCENLPGSFRCTCAQGYAPAPDG
RSCLDVDECEAGDVCDNGICSNTPGSFQCQCLSGYHLSRDRSHCEDIDECDFPAACIGGD
CINTNGSYRCLCPQGHRLVGGRKCQDIDECSQDPSLCLPHGACKNLQGSYVCVCDEGFTP
TQDQHGCEEVEQPHHKKECYLNFDDTVFCDSVLATNVTQQECCCSLGAGWGDHCEIYPCP
VYSSAEFHSLCPDGKGYTQDNNIVNYGIPAHRDIDECMLFGSEICKEGKCVNTQPGYECY
CKQGFYYDGNLLECVDVDECLDESNCRNGVCENTRGGYRCACTPPAEYSPAQRQCLSPEE
MDVDECQDPAACRPGRCVNLPGSYRCECRPPWVPGPSGRDCQLPESPAERAPERRDVCWS
QRGEDGMCAGPLAGPALTFDDCCCRQGRGWGAQCRPCPPRGAGSHCPTSQSESNSFWDTS
PLLLGKPPRDEDSSEEDSDECRCVSGRCVPRPGGAVCECPGGFQLDASRARCVDIDECRE
LNQRGLLCKSERCVNTSGSFRCVCKAGFARSRPHGACVPQRRR

Sequence length

1303

Interactions

View interactions

	Reactome
			Molecules associated with elastic fibres

1207

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Amelogenesis imperfecta	Likely pathogenic	rs2496112558	RCV002282705
Brachyolmia-amelogenesis imperfecta syndrome	Likely pathogenic; Pathogenic	rs2135125210, rs2135143557, rs2135143551, rs1347418307, rs2135157363, rs767708438, rs1275684003, rs766900840, rs2135155640, rs2135120937, rs2135159627, rs1363345814, rs2135130818, rs757974017, rs2496138515 View all (39 more)	RCV001378750 RCV001789734 RCV002038946 RCV001943259 RCV001937049 RCV001938346 RCV001961803 RCV001964020 RCV002035451 RCV001946646 RCV001906000 RCV002049317 RCV001985077 RCV001988471 RCV002282707 RCV002305873 RCV003037407 RCV002612434 RCV002662504 RCV002681333 RCV000186561 RCV000186562 RCV000186563 RCV000186564 RCV000186565 RCV000186566 RCV002770232 RCV002825349 RCV002870751 RCV002842503 RCV002852526 RCV002876865 RCV002858374 RCV002894559 RCV002937949 RCV000007997 RCV005090148 RCV003154862 RCV003154868 RCV003592465 RCV003591241 RCV003591313 RCV003755203 RCV003755298 RCV003755529 RCV003755580 RCV003755594 RCV003755795 RCV003755769 RCV003755977 RCV003756217 RCV003818401 RCV003853572 RCV003876726 RCV000627066 RCV000627067
Gastric cancer	Likely pathogenic	rs766900840	RCV005926457
Geleophysic dysplasia 1	Likely pathogenic; Pathogenic	rs1265250025	RCV006266891
Geleophysic dysplasia 3	Likely pathogenic; Pathogenic	rs2135125210, rs2135141843, rs1554971742, rs1188540819	RCV001824960 RCV001789733 RCV000519031 RCV000520920
Heritable Thoracic Aortic Disease	Pathogenic	rs1286042594, rs1554973844	RCV001291427 RCV001291428
LTBP3-related disorder	Likely pathogenic; Pathogenic	rs1463397648, rs2496175522, rs2496117212	RCV003404114 RCV003397718 RCV003983374

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign	rs182705867	RCV005925786
Geleophysic dysplasia	Uncertain significance	rs937223382	RCV003994593
Hepatocellular carcinoma	Likely benign	rs754482985	RCV005928761
Intellectual disability	Conflicting classifications of pathogenicity	rs370306373	RCV005626524
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs145046881	RCV005907113
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	rs145046881	RCV005907114

Show/Hide Text Mining Associations (32)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Acromicric dysplasia	Associate	33082559
Alcohol Related Disorders	Associate	34906192
Amelogenesis Imperfecta	Associate	34573388
Androgen Insensitivity Syndrome	Associate	25313366
Anemia Aplastic	Associate	35352826
Aneurysm	Associate	35352826
Anodontia	Associate	34573388, 35352826
Aortic Dissection	Associate	34906192
Aortic Valve Stenosis	Associate	34573388
Brachyolmia	Associate	35352826
Cardiomyopathy Hypertrophic	Associate	34573388
Colorectal Neoplasms	Associate	28058013
Deafness oligodontia syndrome	Associate	19344874
Dissection Thoracic Aorta	Associate	35352826
Epilepsy	Associate	40591616
Exfoliation Syndrome	Stimulate	34964803
Growth Disorders	Associate	34906192, 35352826
Heart Septal Defects Atrial	Associate	35352826
HEM dysplasia	Associate	34573388, 34906192
HIV Infections	Associate	36123690
Malar hypoplasia	Associate	35352826
Multiple Myeloma	Associate	25187517
Neoplasms	Associate	32108034
Osteoarthritis	Associate	32452514
Osteoarthritis Hip	Associate	32452514
Osteomas Of Mandible	Associate	35352826
Seizures	Associate	37862918, 40591616
Shoulder Dislocation	Associate	35352826
Stomach Neoplasms	Associate	34983559
Tooth Agenesis Selective 6	Associate	35352826
Tricuspid Valve Prolapse	Associate	35352826
Trigeminal Neuralgia	Associate	38158702

LTBP3 (latent transforming growth factor beta binding protein 3)