ENSG00000127616


Homo sapiens

Features
Gene ID: ENSG00000127616
  
Biological name :SMARCA4
  
Synonyms : P51532 / SMARCA4 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 19
Strand: 1
Band: p13.2
Gene start: 10960825
Gene end: 11079426
  
Corresponding Affymetrix probe sets: 1569073_x_at (Human Genome U133 Plus 2.0 Array)   208793_x_at (Human Genome U133 Plus 2.0 Array)   208794_s_at (Human Genome U133 Plus 2.0 Array)   212520_s_at (Human Genome U133 Plus 2.0 Array)   213719_s_at (Human Genome U133 Plus 2.0 Array)   213720_s_at (Human Genome U133 Plus 2.0 Array)   214360_at (Human Genome U133 Plus 2.0 Array)   214728_x_at (Human Genome U133 Plus 2.0 Array)   215714_s_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000493925
Ensembl peptide - ENSP00000467200
Ensembl peptide - ENSP00000467796
Ensembl peptide - ENSP00000493521
Ensembl peptide - ENSP00000493615
Ensembl peptide - ENSP00000493690
Ensembl peptide - ENSP00000493905
Ensembl peptide - ENSP00000493975
Ensembl peptide - ENSP00000494154
Ensembl peptide - ENSP00000494159
Ensembl peptide - ENSP00000494341
Ensembl peptide - ENSP00000494353
Ensembl peptide - ENSP00000494463
Ensembl peptide - ENSP00000494603
Ensembl peptide - ENSP00000494676
Ensembl peptide - ENSP00000494772
Ensembl peptide - ENSP00000494915
Ensembl peptide - ENSP00000495197
Ensembl peptide - ENSP00000495355
Ensembl peptide - ENSP00000495368
Ensembl peptide - ENSP00000495457
Ensembl peptide - ENSP00000495536
Ensembl peptide - ENSP00000495548
Ensembl peptide - ENSP00000495599
Ensembl peptide - ENSP00000495802
Ensembl peptide - ENSP00000496004
Ensembl peptide - ENSP00000496074
Ensembl peptide - ENSP00000496135
Ensembl peptide - ENSP00000496176
Ensembl peptide - ENSP00000496190
Ensembl peptide - ENSP00000496230
Ensembl peptide - ENSP00000496331
Ensembl peptide - ENSP00000496498
Ensembl peptide - ENSP00000496635
Ensembl peptide - ENSP00000496682
Ensembl peptide - ENSP00000343896
Ensembl peptide - ENSP00000392837
Ensembl peptide - ENSP00000395654
Ensembl peptide - ENSP00000397783
Ensembl peptide - ENSP00000414727
Ensembl peptide - ENSP00000445036
Ensembl peptide - ENSP00000464778
Ensembl peptide - ENSP00000466963
NCBI entrez gene - 6597     See in Manteia.
OMIM - 603254
RefSeq - NM_001128847
RefSeq - NM_001128848
RefSeq - NM_001128849
RefSeq - NM_003072
RefSeq - XM_017027160
RefSeq - XM_017027161
RefSeq - XM_017027162
RefSeq - XM_017027163
RefSeq - XM_017027164
RefSeq - XM_017027165
RefSeq - XM_017027166
RefSeq - XM_017027167
RefSeq - XM_017027168
RefSeq - XM_006722845
RefSeq - XM_006722846
RefSeq - XM_011528198
RefSeq - NM_001128844
RefSeq - NM_001128845
RefSeq - NM_001128846
RefSeq Peptide - NP_001122318
RefSeq Peptide - NP_001122320
RefSeq Peptide - NP_001122321
RefSeq Peptide - NP_003063
RefSeq Peptide - NP_001122316
RefSeq Peptide - NP_001122317
RefSeq Peptide - NP_001122319
swissprot - Q9HBD4
swissprot - K7EP28
swissprot - K7EQF0
swissprot - A0A0A0MT49
swissprot - P51532
swissprot - A7E2E1
Ensembl - ENSG00000127616
  
Related genetic diseases (OMIM): 613325 - {Rhabdoid tumor predisposition syndrome 2}, 613325
  614609 - Coffin-Siris syndrome 4, 614609
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 SMARCA4ENSDARG00000104339Danio rerio
 smarca4aENSDARG00000077226Danio rerio
 Q3TKT4ENSMUSG00000032187Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
P51531 / SMARCA2 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2ENSG0000008050374


Protein motifs (from Interpro)
Interpro ID Name
 IPR000330  SNF2-related, N-terminal domain
 IPR001487  Bromodomain
 IPR001650  Helicase, C-terminal
 IPR006576  BRK domain
 IPR014001  Helicase superfamily 1/2, ATP-binding domain
 IPR014012  Helicase/SANT-associated domain
 IPR014978  Glutamine-Leucine-Glutamine, QLQ
 IPR018359  Bromodomain, conserved site
 IPR027417  P-loop containing nucleoside triphosphate hydrolase
 IPR029295  Snf2, ATP coupling domain
 IPR030100  SWI/SNF complex subunit BRG1
 IPR036427  Bromodomain-like superfamily
 IPR037259  BRK domain superfamily


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0000122 negative regulation of transcription by RNA polymerase II TAS
 biological_processGO:0001188 RNA polymerase I transcriptional preinitiation complex assembly IEA
 biological_processGO:0003407 neural retina development IEP
 biological_processGO:0006325 chromatin organization TAS
 biological_processGO:0006337 nucleosome disassembly IDA
 biological_processGO:0006338 chromatin remodeling IMP
 biological_processGO:0006351 transcription, DNA-templated IEA
 biological_processGO:0006355 regulation of transcription, DNA-templated IEA
 biological_processGO:0006357 regulation of transcription by RNA polymerase II NAS
 biological_processGO:0006366 transcription by RNA polymerase II IEA
 biological_processGO:0007399 nervous system development IEA
 biological_processGO:0030177 positive regulation of Wnt signaling pathway IMP
 biological_processGO:0030308 negative regulation of cell growth IMP
 biological_processGO:0038111 interleukin-7-mediated signaling pathway TAS
 biological_processGO:0043044 ATP-dependent chromatin remodeling IEA
 biological_processGO:0043923 positive regulation by host of viral transcription IMP
 biological_processGO:0045892 negative regulation of transcription, DNA-templated IMP
 biological_processGO:0045893 positive regulation of transcription, DNA-templated IMP
 biological_processGO:0045944 positive regulation of transcription by RNA polymerase II IGI
 biological_processGO:0051091 positive regulation of DNA-binding transcription factor activity IDA
 biological_processGO:0060766 negative regulation of androgen receptor signaling pathway IMP
 biological_processGO:1901838 positive regulation of transcription of nucleolar large rRNA by RNA polymerase I IMP
 biological_processGO:1902661 positive regulation of glucose mediated signaling pathway IDA
 biological_processGO:1902895 positive regulation of pri-miRNA transcription by RNA polymerase II IMP
 biological_processGO:1904837 beta-catenin-TCF complex assembly TAS
 cellular_componentGO:0000790 nuclear chromatin IDA
 cellular_componentGO:0005615 extracellular space HDA
 cellular_componentGO:0005634 nucleus IEA
 cellular_componentGO:0005654 nucleoplasm TAS
 cellular_componentGO:0005730 nucleolus IDA
 cellular_componentGO:0016020 membrane HDA
 cellular_componentGO:0016514 SWI/SNF complex IEA
 cellular_componentGO:0032991 protein-containing complex HDA
 cellular_componentGO:0071564 npBAF complex IDA
 cellular_componentGO:0071565 nBAF complex ISS
 molecular_functionGO:0000166 nucleotide binding IEA
 molecular_functionGO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding HDA
 molecular_functionGO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding HDA
 molecular_functionGO:0001164 RNA polymerase I CORE element sequence-specific DNA binding IDA
 molecular_functionGO:0002039 p53 binding IPI
 molecular_functionGO:0003713 transcription coactivator activity NAS
 molecular_functionGO:0003714 transcription corepressor activity IDA
 molecular_functionGO:0004386 helicase activity TAS
 molecular_functionGO:0005515 protein binding IEA
 molecular_functionGO:0005524 ATP binding IEA
 molecular_functionGO:0008094 DNA-dependent ATPase activity IGI
 molecular_functionGO:0008134 transcription factor binding IPI
 molecular_functionGO:0016787 hydrolase activity IEA
 molecular_functionGO:0016817 hydrolase activity, acting on acid anhydrides IEA
 molecular_functionGO:0016887 ATPase activity IEA
 molecular_functionGO:0030957 Tat protein binding IPI
 molecular_functionGO:0031492 nucleosomal DNA binding HDA
 molecular_functionGO:0042393 histone binding IEA
 molecular_functionGO:0047485 protein N-terminus binding IPI
 molecular_functionGO:0050681 androgen receptor binding IPI
 molecular_functionGO:0070182 DNA polymerase binding IPI
 molecular_functionGO:0070577 lysine-acetylated histone binding IDA


Pathways (from Reactome)
Pathway description
Interleukin-7 signaling
Formation of the beta-catenin:TCF transactivating complex
RMTs methylate histone arginines
Chromatin modifying enzymes
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000006 Autosomal dominant inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in heterozygotes. In the context of medical genetics, an autosomal dominant disorder is caused when a single copy of the mutant allele is present. Males and females are affected equally, and can both transmit the disorder with a risk of 50% for each child of inheriting the mutant allele." [HPO:curators]
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 HP:0000028 Cryptorchidism "Absence of one or both testes from the scrotum owing to failure of the testis or testes to descend through the inguinal canal to the testis." [HPO:curators]
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 HP:0000086 Ectopic kidney "A developmental defect in which a kidney is located in an abnormal anatomic position." [HPO:curators]
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 HP:0000126 Hydronephrosis 
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 HP:0000154 Wide mouth "Abnormally wide mouth." [HPO:curators]
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 HP:0000158 Macroglossia "Increased length and width of the tongue." [pmid:19125428]
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 HP:0000164 Abnormality of the teeth "Any abnormality of the primary (deciduous) or permanent teeth." [HPO:curators]
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 HP:0000175 Cleft palate "Cleft palate is a developmental defect of the `palate` (FMA:54549) resulting from a failure of fusion of the palatine processes." [HPO:curators]
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 HP:0000179 Prominent lower lip "Increased thickness of the lower lip, leading to a prominent appearance of the lower lip." [HPO:curators]
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 HP:0000252 Microcephaly "Microcephaly is a neurodevelopmental disorder in which the circumference of the head is more than two standard deviations smaller than the age- and gender-dependent norm." [HPO:curators]
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 HP:0000280 Coarse facial features 
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 HP:0000286 Epicanthus "An epicanthal fold is a semilunar fold of skin that extends from the upper eyelid across the medial canthal area to the lower eyelid." [HPO:curators]
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 HP:0000322 Short philtrum 
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 HP:0000365 Hearing loss 
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 HP:0000431 Broad nasal bridge "Increased horizontal dimension of the upper, bony part of the nose." [HPO:curators]
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 HP:0000445 Broad nose 
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 HP:0000457 Flat nose 
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 HP:0000463 Nares, anteverted "Anteriorly-facing nostrils viewed with the head in the Frankfurt horizontal and the eyes of the observer level with the eyes of the subject." [pmid:19152422]
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 HP:0000486 Strabismus "Strabismus (also known as squint) is a condition in which the eyes are not properly aligned with each other." [HPO:curators]
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 HP:0000505 Impaired vision 
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 HP:0000508 Ptosis "Drooping of the eyelid." [HPO:curators]
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 HP:0000518 Cataract "A cataract is an opacity or clouding that develops in the crystalline `lens` (FMA:58241) of the eye or in its `capsule` (FMA:58881)." [HPO:probinson]
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 HP:0000527 Long eyelashes "Mid upper eyelash length >10 mm or increased length of the eyelashes (subjective)." [pmid:19125427]
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 HP:0000574 Thick eyebrows 
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 HP:0000632 Lacrimation abnormality 
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 HP:0000639 Nystagmus "Rhythmic, involuntary oscillations of one or both eyes related to abnormality in fixation, conjugate gaze, or vestibular mechanisms." [HPO:curators]
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 HP:0000776 Diaphragmatic hernia "Diaphragmatic hernia is the result of a developmental defect causing an abnormal opening in the diaphragm, through which abdominal organs (stomach, spleen, liver, and intestines) can protrude into the thoracic cavity. This usually causes respiratory distress in the newborn period." [HPO:curators]
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 HP:0000889 Abnormality of the clavicles "Any abnormality of the clavicles (collar bones)." [HPO:curators]
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 HP:0000965 Cutis marmorata 
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 HP:0000998 Hypertrichosis "Hypertrichosis is increased hair growth that is abnormal in quantity or location." [HPO:curators]
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 HP:0001007 Hirsutism "Abnormally increased hair growth." [HPO:curators]
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 HP:0001249 Mental retardation 
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 HP:0001250 Seizures "Seizures are an intermittent `abnormality of the central nervous system` (FMA:HP:0002011) due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements." [HPO:probinson]
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 HP:0001252 Muscular hypotonia "Muscular hypotonia is an abnormally low muscle tone (the amount of tension or resistance to movement in a muscle), often involving reduced muscle strength. Hypotonia is characterized by a diminished resistance to passive stretching." [HPO:curators]
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 HP:0001263 Developmental retardation "A delay in the achievement of motor or mental milestones manifested prior to age 18 and generally associated with lifelong mental and/or physical impairments." [HPO:curators]
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 HP:0001273 Abnormality of the corpus callosum "Abnormality of the corpus callosum, which is a broad thick band of nerve fibers that connects the right and left cerebral hemispheres." [HPO:curators]
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 HP:0001290 Generalized hypotonia "Generalized muscular hypotonia (abnormally low muscle tone)." [HPO:curators]
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 HP:0001305 Dandy-Walker malformation "A congenital brain malformation typically characterized by incomplete formation of the cerebellar vermis, dilation of the fourth ventricle, and enlargement of the posterior fossa. In layman s terms, Dandy Walker malformation is a cyst in the cerebellum (typically symmetrical) that is involved with the fourth ventricle. This may interfere with the body s ability to drain cerebrospinal fluid from the brain, resulting in hydrocephalus. Dandy Walker cysts are formed during early embryonic development, while the brain forms. The cyst in the cerebellum typically has several blood vessels running through it connecting to the brain, thereby prohibiting surgical removal." [HPO:curators]
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 HP:0001338 Partial agenesis of the corpus callosum "A partial failure of the development of the corpus callosum." [HPO:curators]
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 HP:0001511 Intrauterine growth retardation 
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 HP:0002079 Hypoplasia of the corpus callosum "Underdevelopment of the corpus callosum." [HPO:curators]
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 HP:0002205 Recurrent respiratory infections 
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 HP:0002209 Sparse scalp hair "Sparseness of the `head hair` (FMA:54241)." [HPO:probinson]
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 HP:0002217 Slow-growing hair 
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 HP:0002230 Generalized hirsutism "Abnormally increased hair growth over much of the entire body." [HPO:curators]
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 HP:0002650 Scoliosis "The presence of an abnormal lateral curvature of the spine." [HPO:curators]
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 HP:0002673 Coxa valga "Coxa valga is a deformity of the hip in which the angle between the femoral shaft and the femoral neck is increased compared to age-adjusted values (about 150 degrees in newborns gradually reducing to 120-130 degrees in adults)." [HPO:curators]
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 HP:0002750 Delayed skeletal maturation "A decreased rate of skeletal maturation. Delayed skeletal maturation can be diagnosed on the basis of an estimation of the bone age from radiographs of specific bones in the human body." [HPO:curators]
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 HP:0002808 Kyphosis 
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 HP:0003042 Elbow dislocation "A dislocation affecting the elbow joint, where the radius, ulna, and humerus meet." [HPO:curators]
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 HP:0003272 Abnormality of the hip "An abnormality of the hip joint or the surrounding anatomic region." [HPO:curators]
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 HP:0003298 Spina bifida occulta "The closed form of spina bifida." [HPO:curators]
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 HP:0004322 Decreased body height "A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms)." [HPO:curators]
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 HP:0005108 Abnormality of the intervertebral disks 
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 HP:0005280 Depressed nasal root and bridge 
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 HP:0005692 Joint hyperflexibility 
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 HP:0006498 Aplasia/Hypoplasia of the patella "Absence or underdevelopment of the patella." [HPO:curators]
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 HP:0007360 Aplasia/Hypoplasia of the cerebellum 
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 HP:0007598 Bilateral single palmar creases 
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 HP:0008398 Hypoplastic to absent fifth finger- and toenails 
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 HP:0008678 Renal hypoplasia/aplasia 
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 HP:0008872 Feeding problems in infancy 
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 HP:0009239 Aplasia/Hypoplasia of the distal phalanx of the 5th finger 
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 HP:0009835 Aplasia/Hypoplasia of the distal phalanges of the hand "Absence or underdevelopment of the distal phalanges." [HPO:curators]
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 HP:0009882 Hypoplasia of the distal phalanges of the hand 
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 HP:0009928 Ala nasi, thick "Increase in bulk of the ala nasi." [pmid:19152422]
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 HP:0011937 Hypoplastic fifth toenail "Underdeveloped nails of the fifth toes." [HPO:probinson]
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 HP:0011968 Feeding difficulties "Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it." [ISCA:eriggs]
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 HP:0030680 Abnormality of cardiovascular system morphology "Any structural anomaly of the heart and great vessels." []
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 HP:0100371 Aplasia/Hypoplasia of the distal phalanx of the 5th toe 
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000100462 PRMT5 / O14744 / protein arginine methyltransferase 5  / complex / reaction
 ENSG00000116455 WDR77 / Q9BQA1 / WD repeat domain 77  / complex / reaction
 ENSG00000173473 Q92922 / SMARCC1 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 1  / complex
 ENSG00000099956 Q12824 / SMARCB1 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1  / complex
 ENSG00000138795 LEF1 / Q9UJU2 / lymphoid enhancer binding factor 1  / complex / reaction
 ENSG00000164362 TERT / O14746 / telomerase reverse transcriptase  / complex / reaction
 ENSG00000067955 CBFB / Q13951 / core-binding factor beta subunit  / reaction / complex
 ENSG00000159216 RUNX1 / Q01196 / runt related transcription factor 1  / reaction / complex
 ENSG00000148737 Q9NQB0 / TCF7L2 / transcription factor 7 like 2  / reaction / complex
 ENSG00000185658 BRWD1 / Q9NSI6 / bromodomain and WD repeat domain containing 1  / reaction / complex
 ENSG00000139613 Q8TAQ2 / SMARCC2 / SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2  / complex
 ENSG00000168036 CTNNB1 / P35222 / catenin beta 1  / reaction / complex






 

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