Seroatlas · Human Serome Atlas

ARID1A

AT-rich interactive domain-containing protein 1A

Also known as: ARI1A_HUMAN, B120, BAF250, BAF250a, C10rf4, C1orf4, P270, SMARCF1

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O14497
Gene: ARID1A
Ensembl: ENSG00000117713
Chromosome: 1
Canonical length: 2285 aa
Protein class: Cancer-related genes, Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

This gene encodes a member of the SWI/SNF family, whose members have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. It possesses at least two conserved domains that could be important for its function. First, it has a DNA-binding domain that can specifically bind an AT-rich DNA sequence known to be recognized by a SNF/SWI complex at the beta-globin locus. Second, the C-terminus of the protein can stimulate glucocorticoid receptor-dependent transcriptional activation. It is thought that the protein encoded by this gene confers specificity to the SNF/SWI complex and may recruit the complex to its targets through either protein-DNA or protein-protein interactions. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

2285 residues, UniProt reviewed canonical sequence.

>O14497|ARID1A
     1  MAAQVAPAAA SSLGNPPPPP PSELKKAEQQ QREEAGGEAA AAAAAERGEM KAAAGQESEG
    61  PAVGPPQPLG KELQDGAESN GGGGGGGAGS GGGPGAEPDL KNSNGNAGPR PALNNNLTEP
   121  PGGGGGGSSD GVGAPPHSAA AALPPPAYGF GQPYGRSPSA VAAAAAAVFH QQHGGQQSPG
   181  LAALQSGGGG GLEPYAGPQQ NSHDHGFPNH QYNSYYPNRS AYPPPAPAYA LSSPRGGTPG
   241  SGAAAAAGSK PPPSSSASAS SSSSSFAQQR FGAMGGGGPS AAGGGTPQPT ATPTLNQLLT
   301  SPSSARGYQG YPGGDYSGGP QDGGAGKGPA DMASQCWGAA AAAAAAAAAS GGAQQRSHHA
   361  PMSPGSSGGG GQPLARTPQP SSPMDQMGKM RPQPYGGTNP YSQQQGPPSG PQQGHGYPGQ
   421  PYGSQTPQRY PMTMQGRAQS AMGGLSYTQQ IPPYGQQGPS GYGQQGQTPY YNQQSPHPQQ
   481  QQPPYSQQPP SQTPHAQPSY QQQPQSQPPQ LQSSQPPYSQ QPSQPPHQQS PAPYPSQQST
   541  TQQHPQSQPP YSQPQAQSPY QQQQPQQPAP STLSQQAAYP QPQSQQSQQT AYSQQRFPPP
   601  QELSQDSFGS QASSAPSMTS SKGGQEDMNL SLQSRPSSLP DLSGSIDDLP MGTEGALSPG
   661  VSTSGISSSQ GEQSNPAQSP FSPHTSPHLP GIRGPSPSPV GSPASVAQSR SGPLSPAAVP
   721  GNQMPPRPPS GQSDSIMHPS MNQSSIAQDR GYMQRNPQMP QYSSPQPGSA LSPRQPSGGQ
   781  IHTGMGSYQQ NSMGSYGPQG GQYGPQGGYP RQPNYNALPN ANYPSAGMAG GINPMGAGGQ
   841  MHGQPGIPPY GTLPPGRMSH ASMGNRPYGP NMANMPPQVG SGMCPPPGGM NRKTQETAVA
   901  MHVAANSIQN RPPGYPNMNQ GGMMGTGPPY GQGINSMAGM INPQGPPYSM GGTMANNSAG
   961  MAASPEMMGL GDVKLTPATK MNNKADGTPK TESKSKKSSS STTTNEKITK LYELGGEPER
  1021  KMWVDRYLAF TEEKAMGMTN LPAVGRKPLD LYRLYVSVKE IGGLTQVNKN KKWRELATNL
  1081  NVGTSSSAAS SLKKQYIQCL YAFECKIERG EDPPPDIFAA ADSKKSQPKI QPPSPAGSGS
  1141  MQGPQTPQST SSSMAEGGDL KPPTPASTPH SQIPPLPGMS RSNSVGIQDA FNDGSDSTFQ
  1201  KRNSMTPNPG YQPSMNTSDM MGRMSYEPNK DPYGSMRKAP GSDPFMSSGQ GPNGGMGDPY
  1261  SRAAGPGLGN VAMGPRQHYP YGGPYDRVRT EPGIGPEGNM STGAPQPNLM PSNPDSGMYS
  1321  PSRYPPQQQQ QQQQRHDSYG NQFSTQGTPS GSPFPSQQTT MYQQQQQNYK RPMDGTYGPP
  1381  AKRHEGEMYS VPYSTGQGQP QQQQLPPAQP QPASQQQAAQ PSPQQDVYNQ YGNAYPATAT
  1441  AATERRPAGG PQNQFPFQFG RDRVSAPPGT NAQQNMPPQM MGGPIQASAE VAQQGTMWQG
  1501  RNDMTYNYAN RQSTGSAPQG PAYHGVNRTD EMLHTDQRAN HEGSWPSHGT RQPPYGPSAP
  1561  VPPMTRPPPS NYQPPPSMQN HIPQVSSPAP LPRPMENRTS PSKSPFLHSG MKMQKAGPPV
  1621  PASHIAPAPV QPPMIRRDIT FPPGSVEATQ PVLKQRRRLT MKDIGTPEAW RVMMSLKSGL
  1681  LAESTWALDT INILLYDDNS IMTFNLSQLP GLLELLVEYF RRCLIEIFGI LKEYEVGDPG
  1741  QRTLLDPGRF SKVSSPAPME GGEEEEELLG PKLEEEEEEE VVENDEEIAF SGKDKPASEN
  1801  SEEKLISKFD KLPVKIVQKN DPFVVDCSDK LGRVQEFDSG LLHWRIGGGD TTEHIQTHFE
  1861  SKTELLPSRP HAPCPPAPRK HVTTAEGTPG TTDQEGPPPD GPPEKRITAT MDDMLSTRSS
  1921  TLTEDGAKSS EAIKESSKFP FGISPAQSHR NIKILEDEPH SKDETPLCTL LDWQDSLAKR
  1981  CVCVSNTIRS LSFVPGNDFE MSKHPGLLLI LGKLILLHHK HPERKQAPLT YEKEEEQDQG
  2041  VSCNKVEWWW DCLEMLRENT LVTLANISGQ LDLSPYPESI CLPVLDGLLH WAVCPSAEAQ
  2101  DPFSTLGPNA VLSPQRLVLE TLSKLSIQDN NVDLILATPP FSRLEKLYST MVRFLSDRKN
  2161  PVCREMAVVL LANLAQGDSL AARAIAVQKG SIGNLLGFLE DSLAATQFQQ SQASLLHMQN
  2221  PPFEPTSVDM MRRAARALLA LAKVDENHSE FTLYESRLLD ISVSPLMNSL VSQVICDVLF
  2281  LIGQS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against ARID1A can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.58
Highest tissue expression: 43 nTPM

Expression across tissuesHPA

Tissue

thymus: 43 nTPM
bone marrow: 35 nTPM
lymph node: 24 nTPM
spleen: 23 nTPM
tonsil: 22 nTPM
pancreas: 22 nTPM

Single-cell type

neutrophils: 362 nCPM
monocyte progenitors: 319 nCPM
neutrophil progenitors: 282 nCPM
thymocytes: 236 nCPM
microglia: 235 nCPM
erythrocyte progenitors: 205 nCPM

Immune cell

neutrophil: 3.3 nTPM
plasmacytoid DC: 2.4 nTPM
MAIT T-cell: 2.1 nTPM
memory CD8 T-cell: 2.1 nTPM
NK-cell: 2 nTPM
naive CD8 T-cell: 1.9 nTPM

Brain region

cerebral cortex: 242 nTPM
hypothalamus: 191 nTPM
medulla oblongata: 163 nTPM
thalamus: 144 nTPM
pons: 135 nTPM
amygdala: 135 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about ARID1A.

Disease | AllUniProt

Conditions ARID1A is implicated in, by any mechanism.

Coffin-Siris syndrome 2 (CSS2) MIM:614607

Disease | GeneticClinVar

143 pathogenic / likely-pathogenic of 1,938 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Intellectual disability, autosomal dominant 14
Malignant tumor of urinary bladder
Inborn genetic diseases
ARID1A-related BAFopathy
Neoplasm

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.07
gnomAD pLI: 1
gnomAD missense Z: 3.66
DepMap mean gene effect: -0.24
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

ARID DNA-binding domain
Armadillo-like helical
Armadillo-type fold
SWI/SNF-like complex subunit BAF250/Osa
SWI/SNF-like complex subunit BAF250, C-terminal
ARID DNA-binding domain superfamily
ARID/BRIGHT DNA binding domain
SWI/SNF-like complex subunit BAF250/Osa
AT-rich interactive domain-containing protein 1A, ARID/BRIGHT DNA binding domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of ARID1A in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads ARID1A as an antibody target. Whether an autoantibody or antibody against ARID1A could matter depends on whether native ARID1A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

ARID1A is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label ARID1A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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