VCL (vinculin)

Gene

• Entrez ID: 7414
• Gene name: Vinculin
• Gene symbol: VCL
• Synonyms: CMD1W, CMH15, HEL114, MV, MVCL
• Chromosome: 10
• Chromosome location: 10q22.2
• Summary: Vinculin is a cytoskeletal protein associated with cell-cell and cell-matrix junctions, where it is thought to function as one of several interacting proteins involved in anchoring F-actin to the membrane. Defects in VCL are the cause of cardiomyopathy dilated type 1W. Dilated cardiomyopathy is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs71579374	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Missense variant, coding sequence variant
rs71579375	C>A,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Intron variant, coding sequence variant, missense variant
rs121917776	C>T	Pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs141033098	A>C	Benign-likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs150385900	G>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity, benign, benign-likely-benign	Coding sequence variant, missense variant
rs189242810	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Coding sequence variant, missense variant
rs200624351	C>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs367598954	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs373744314	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs397517237	GTT>-	Likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion, intron variant
rs397517244	C>T	Likely-pathogenic, uncertain-significance	Coding sequence variant, stop gained
rs397517245	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs727503738	A>G	Likely-pathogenic	Splice acceptor variant
rs727503741	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs727504381	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs779488376	A>-	Uncertain-significance, likely-pathogenic	Coding sequence variant, frameshift variant
rs781036800	CT>-	Uncertain-significance, likely-pathogenic	Coding sequence variant, intron variant, frameshift variant
rs863225121	G>T	Likely-pathogenic	Coding sequence variant, missense variant
rs876657674	->G	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT004114	hsa-miR-661	Western blot	19584269
MIRT004115	hsa-miR-559	Western blot	19584269
MIRT025522	hsa-miR-34a-5p	Proteomics	21566225
MIRT036206	hsa-miR-320b	CLASH	23622248
MIRT038322	hsa-miR-130b-5p	CLASH	23622248
MIRT044534	hsa-miR-320a	CLASH	23622248
MIRT045944	hsa-miR-125b-5p	CLASH	23622248
MIRT046654	hsa-miR-222-3p	CLASH	23622248
MIRT048250	hsa-miR-196a-5p	CLASH	23622248
MIRT051181	hsa-miR-16-5p	CLASH	23622248
MIRT051181	hsa-miR-16-5p	HITS-CLIP	22473208
MIRT464248	hsa-miR-6811-5p	PAR-CLIP	23592263
MIRT464249	hsa-miR-6511b-5p	PAR-CLIP	23592263
MIRT464250	hsa-miR-7151-3p	PAR-CLIP	23592263
MIRT464251	hsa-miR-5095	PAR-CLIP	23592263
MIRT464252	hsa-miR-8065	PAR-CLIP	23592263
MIRT464253	hsa-miR-656-5p	PAR-CLIP	23592263
MIRT464254	hsa-miR-6799-5p	PAR-CLIP	23592263
MIRT464255	hsa-miR-6722-3p	PAR-CLIP	23592263
MIRT464256	hsa-miR-6836-5p	PAR-CLIP	23592263
MIRT464257	hsa-miR-1909-3p	PAR-CLIP	23592263
MIRT464258	hsa-miR-6132	PAR-CLIP	23592263
MIRT464259	hsa-miR-98-5p	PAR-CLIP	23592263
MIRT464260	hsa-miR-4500	PAR-CLIP	23592263
MIRT464261	hsa-miR-4458	PAR-CLIP	23592263
MIRT464262	hsa-let-7i-5p	PAR-CLIP	23592263
MIRT464263	hsa-let-7g-5p	PAR-CLIP	23592263
MIRT464264	hsa-let-7f-5p	PAR-CLIP	23592263
MIRT464265	hsa-let-7e-5p	PAR-CLIP	23592263
MIRT464266	hsa-let-7d-5p	PAR-CLIP	23592263
MIRT464267	hsa-let-7c-5p	PAR-CLIP	23592263
MIRT464268	hsa-let-7b-5p	PAR-CLIP	23592263
MIRT464269	hsa-let-7a-5p	PAR-CLIP	23592263
MIRT464270	hsa-miR-6754-5p	PAR-CLIP	23592263
MIRT464271	hsa-miR-4441	PAR-CLIP	23592263
MIRT464272	hsa-miR-4270	PAR-CLIP	23592263
MIRT464273	hsa-miR-6504-3p	PAR-CLIP	23592263
MIRT464274	hsa-miR-4739	PAR-CLIP	23592263
MIRT464275	hsa-miR-4756-5p	PAR-CLIP	23592263
MIRT464276	hsa-miR-1321	PAR-CLIP	23592263
MIRT464277	hsa-miR-4700-3p	PAR-CLIP	23592263
MIRT726141	hsa-miR-195-5p	HITS-CLIP	22473208
MIRT726142	hsa-miR-15b-5p	HITS-CLIP	22473208
MIRT726143	hsa-miR-15a-5p	HITS-CLIP	22473208

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002009	Process	Morphogenesis of an epithelium	IMP	20086044
GO:0002102	Component	Podosome	IEA
GO:0002162	Function	Dystroglycan binding	IPI	18341635
GO:0002576	Process	Platelet degranulation	TAS
GO:0003779	Function	Actin binding	IDA	16803572
GO:0003779	Function	Actin binding	IDA	7816144
GO:0005198	Function	Structural molecule activity	IEA
GO:0005515	Function	Protein binding	IPI	9054445, 9885244, 10320934, 12473693, 15070891, 15163412, 15988023, 16189514, 16803572, 16826238, 17082770, 17289036, 17932491, 18028034, 21841197, 22427331, 25416956, 26923917, 29892012
GO:0005576	Component	Extracellular region	TAS
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	TAS	16130169
GO:0005911	Component	Cell-cell junction	IMP	25753039
GO:0005911	Component	Cell-cell junction	ISS
GO:0005912	Component	Adherens junction	IDA	20086044, 26923917
GO:0005912	Component	Adherens junction	ISS
GO:0005916	Component	Fascia adherens	IEA
GO:0005925	Component	Focal adhesion	HDA	21423176
GO:0005925	Component	Focal adhesion	IDA	20086044, 29162887
GO:0005925	Component	Focal adhesion	IMP	26923917
GO:0005925	Component	Focal adhesion	ISS
GO:0006936	Process	Muscle contraction	TAS
GO:0007155	Process	Cell adhesion	TAS	15501673
GO:0007160	Process	Cell-matrix adhesion	TAS	20086044
GO:0008013	Function	Beta-catenin binding	ISS	20086044
GO:0030032	Process	Lamellipodium assembly	ISS
GO:0030055	Component	Cell-substrate junction	NAS	2116004
GO:0030336	Process	Negative regulation of cell migration	TAS	15494027
GO:0031625	Function	Ubiquitin protein ligase binding	IPI	19725078
GO:0032991	Component	Protein-containing complex	IDA	9700171
GO:0034333	Process	Adherens junction assembly	IMP	20086044
GO:0034394	Process	Protein localization to cell surface	IMP	20086044
GO:0034774	Component	Secretory granule lumen	TAS
GO:0035580	Component	Specific granule lumen	TAS
GO:0035633	Process	Maintenance of blood-brain barrier	NAS	30280653
GO:0042383	Component	Sarcolemma	ISS
GO:0043034	Component	Costamere	IDA	9415431
GO:0043034	Component	Costamere	ISS
GO:0043297	Process	Apical junction assembly	IMP	9700171
GO:0043312	Process	Neutrophil degranulation	TAS
GO:0044291	Component	Cell-cell contact zone	IMP	26923917
GO:0045294	Function	Alpha-catenin binding	IPI	9700171
GO:0045296	Function	Cadherin binding	HDA	25468996
GO:0045296	Function	Cadherin binding	ISS	20086044
GO:0048675	Process	Axon extension	IEA
GO:0051893	Process	Regulation of focal adhesion assembly	IMP	26923917
GO:0070062	Component	Extracellular exosome	HDA	19056867, 20458337
GO:0070527	Process	Platelet aggregation	HMP	23382103
GO:0090136	Process	Epithelial cell-cell adhesion	IMP	20086044
GO:1903140	Process	Regulation of establishment of endothelial barrier	IDA	26923917
GO:1903561	Component	Extracellular vesicle	HDA	24769233
GO:1904702	Process	Regulation of protein localization to adherens junction	IMP	26923917
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

Other IDs

• MIM: 193065
• HGNC: 12665
• e!Ensembl: ENSG00000035403

Protein

• UniProt ID: P18206
• Protein name: Vinculin (Metavinculin) (MV)
• Protein function: Actin filament (F-actin)-binding protein involved in cell-matrix adhesion and cell-cell adhesion. Regulates cell-surface E-cadherin expression and potentiates mechanosensing by the E-cadherin complex. May also play important roles in cell morphology and locomotion.
• PDB: 1RKC, 1RKE, 1SYQ, 1TR2, 1YDI, 2GWW, 2HSQ, 2IBF, 3H2U, 3H2V, 3JBK, 3MYI, 3RF3, 3S90, 3TJ5, 3TJ6, 3VF0, 4DJ9, 4EHP, 4LN2, 4LNP, 4PR9, 5L0C, 5L0D, 5L0F, 5L0G, 5L0H, 5L0I, 5L0J, 5O2Q, 6FUY, 6UPW, 7KTT, 7KTU, 7KTV, 7KTW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01044	Vinculin	3 → 485	Vinculin family	Family
  PF01044	Vinculin	476 → 921	Vinculin family	Family
  PF01044	Vinculin	918 → 1134	Vinculin family	Family

• Sequence:

  MPVFHTRTIESILEPVAQQISHLVIMHEEGEVDGKAIPDLTAPVAAVQAAVSNLVRVGKE
  TVQTTEDQILKRDMPPAFIKVENACTKLVQAAQMLQSDPYSVPARDYLIDGSRGILSGTS
  DLLLTFDEAEVRKIIRVCKGILEYLTVAEVVETMEDLVTYTKNLGPGMTKMAKMIDERQQ
  ELTHQEHRVMLVNSMNTVKELLPVLISAMKIFVTTKNSKNQGIEEALKNRNFTVEKMSAE
  INEIIRVLQLTSWDEDAWASKDTEAMKRALASIDSKLNQAKGWLRDPSASPGDAGEQAIR
  QILDEAGKVGELCAGKERREILGTCKMLGQMTDQVADLRARGQGSSPVAMQKAQQVSQGL
  DVLTAKVENAARKLEAMTNSKQSIAKKIDAAQNWLADPNGGPEGEEQIRGALAEARKIAE
  LCDDPKERDDILRSLGEISALTSKLADLRRQGKGDSPEARALAKQVATALQNLQTKTNRA
  VANSRPAKAAVHLEGKIEQAQRWIDNPTVDDRGVGQAAIRGLVAEGHRLANVMMGPYRQD
  LLAKCDRVDQLTAQLADLAARGEGESPQARALASQLQDSLKDLKARMQEAMTQEVSDVFS
  DTTTPIKLLAVAATAPPDAPNREEVFDERAANFENHSGKLGATAEKAAAVGTANKSTVEG
  IQASVKTARELTPQVVSAARILLRNPGNQAAYEHFETMKNQWIDNVEKMTGLVDEAIDTK
  SLLDASEEAIKKDLDKCKVAMANIQPQMLVAGATSIARRANRILLVAKREVENSEDPKFR
  EAVKAASDELSKTISPMVMDAKAVAGNISDPGLQKSFLDSGYRILGAVAKVREAFQPQEP
  DFPPPPPDLEQLRLTDELAPPKPPLPEGEVPPPRPPPPEEKDEEFPEQKAGEVINQPMMM
  AARQLHDEARKWSSKPGIPAAEVGIGVVAEADAADAAGFPVPPDMEDDYEPELLLMPSNQ
  PVNQPILAAAQSLHREATKWSSKGNDIIAAAKRMALLMAEMSRLVRGGSGTKRALIQCAK
  DIAKASDEVTRLAKEVAKQCTDKRIRTNLLQVCERIPTISTQLKILSTVKATMLGRTNIS
  DEESEQATEMLVHNAQNLMQSVKETVREAEAASIKIRTDAGFTLRWVRKTPWYQ

• Sequence length: 1134