Seroatlas · Human Serome Atlas

SMG1

Serine/threonine-protein kinase SMG1

Also known as: ATX, KIAA0421, LIP, SMG1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q96Q15
Gene: SMG1
Ensembl: ENSG00000157106
Chromosome: 16
Canonical length: 3661 aa
Protein class: Enzymes, Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013]

Canonical amino-acid sequenceUniProt

3661 residues, UniProt reviewed canonical sequence.

>Q96Q15|SMG1
     1  MSRRAPGSRL SSGGGGGGTK YPRSWNDWQP RTDSASADPD NLKYSSSRDR GGSSSYGLQP
    61  SNSAVVSRQR HDDTRVHADI QNDEKGGYSV NGGSGENTYG RKSLGQELRV NNVTSPEFTS
   121  VQHGSRALAT KDMRKSQERS MSYSDESRLS NLLRRITRED DRDRRLATVK QLKEFIQQPE
   181  NKLVLVKQLD NILAAVHDVL NESSKLLQEL RQEGACCLGL LCASLSYEAE KIFKWIFSKF
   241  SSSAKDEVKL LYLCATYKAL ETVGEKKAFS SVMQLVMTSL QSILENVDTP ELLCKCVKCI
   301  LLVARCYPHI FSTNFRDTVD ILVGWHIDHT QKPSLTQQVS GWLQSLEPFW VADLAFSTTL
   361  LGQFLEDMEA YAEDLSHVAS GESVDEDVPP PSVSLPKLAA LLRVFSTVVR SIGERFSPIR
   421  GPPITEAYVT DVLYRVMRCV TAANQVFFSE AVLTAANECV GVLLGSLDPS MTIHCDMVIT
   481  YGLDQLENCQ TCGTDYIISV LNLLTLIVEQ INTKLPSSFV EKLFIPSSKL LFLRYHKEKE
   541  VVAVAHAVYQ AVLSLKNIPV LETAYKLILG EMTCALNNLL HSLQLPEACS EIKHEAFKNH
   601  VFNVDNAKFV VIFDLSALTT IGNAKNSLIG MWALSPTVFA LLSKNLMIVH SDLAVHFPAI
   661  QYAVLYTLYS HCTRHDHFIS SSLSSSSPSL FDGAVISTVT TATKKHFSII LNLLGILLKK
   721  DNLNQDTRKL LMTWALEAAV LMKKSETYAP LFSLPSFHKF CKGLLANTLV EDVNICLQAC
   781  SSLHALSSSL PDDLLQRCVD VCRVQLVHSG TRIRQAFGKL LKSIPLDVVL SNNNHTEIQE
   841  ISLALRSHMS KAPSNTFHPQ DFSDVISFIL YGNSHRTGKD NWLERLFYSC QRLDKRDQST
   901  IPRNLLKTDA VLWQWAIWEA AQFTVLSKLR TPLGRAQDTF QTIEGIIRSL AAHTLNPDQD
   961  VSQWTTADND EGHGNNQLRL VLLLQYLENL EKLMYNAYEG CANALTSPPK VIRTFFYTNR
  1021  QTCQDWLTRI RLSIMRVGLL AGQPAVTVRH GFDLLTEMKT TSLSQGNELE VTIMMVVEAL
  1081  CELHCPEAIQ GIAVWSSSIV GKNLLWINSV AQQAEGRFEK ASVEYQEHLC AMTGVDCCIS
  1141  SFDKSVLTLA NAGRNSASPK HSLNGESRKT VLSKPTDSSP EVINYLGNKA CECYISIADW
  1201  AAVQEWQNAI HDLKKSTSST SLNLKADFNY IKSLSSFESG KFVECTEQLE LLPGENINLL
  1261  AGGSKEKIDM KKLLPNMLSP DPRELQKSIE VQLLRSSVCL ATALNPIEQD QKWQSITENV
  1321  VKYLKQTSRI AIGPLRLSTL TVSQSLPVLS TLQLYCSSAL ENTVSNRLST EDCLIPLFSE
  1381  ALRSCKQHDV RPWMQALRYT MYQNQLLEKI KEQTVPIRSH LMELGLTAAK FARKRGNVSL
  1441  ATRLLAQCSE VQLGKTTTAQ DLVQHFKKLS TQGQVDEKWG PELDIEKTKL LYTAGQSTHA
  1501  MEMLSSCAIS FCKSVKAEYA VAKSILTLAK WIQAEWKEIS GQLKQVYRAQ HQQNFTGLST
  1561  LSKNILTLIE LPSVNTMEEE YPRIESESTV HIGVGEPDFI LGQLYHLSSV QAPEVAKSWA
  1621  ALASWAYRWG RKVVDNASQG EGVRLLPREK SEVQNLLPDT ITEEEKERIY GILGQAVCRP
  1681  AGIQDEDITL QITESEDNEE DDMVDVIWRQ LISSCPWLSE LDESATEGVI KVWRKVVDRI
  1741  FSLYKLSCSA YFTFLKLNAG QIPLDEDDPR LHLSHRVEQS TDDMIVMATL RLLRLLVKHA
  1801  GELRQYLEHG LETTPTAPWR GIIPQLFSRL NHPEVYVRQS ICNLLCRVAQ DSPHLILYPA
  1861  IVGTISLSSE SQASGNKFST AIPTLLGNIQ GEELLVSECE GGSPPASQDS NKDEPKSGLN
  1921  EDQAMMQDCY SKIVDKLSSA NPTMVLQVQM LVAELRRVTV LWDELWLGVL LQQHMYVLRR
  1981  IQQLEDEVKR VQNNNTLRKE EKIAIMREKH TALMKPIVFA LEHVRSITAA PAETPHEKWF
  2041  QDNYGDAIEN ALEKLKTPLN PAKPGSSWIP FKEIMLSLQQ RAQKRASYIL RLEEISPWLA
  2101  AMTNTEIALP GEVSARDTVT IHSVGGTITI LPTKTKPKKL LFLGSDGKSY PYLFKGLEDL
  2161  HLDERIMQFL SIVNTMFATI NRQETPRFHA RHYSVTPLGT RSGLIQWVDG ATPLFGLYKR
  2221  WQQREAALQA QKAQDSYQTP QNPGIVPRPS ELYYSKIGPA LKTVGLSLDV SRRDWPLHVM
  2281  KAVLEELMEA TPPNLLAKEL WSSCTTPDEW WRVTQSYARS TAVMSMVGYI IGLGDRHLDN
  2341  VLIDMTTGEV VHIDYNVCFE KGKSLRVPEK VPFRMTQNIE TALGVTGVEG VFRLSCEQVL
  2401  HIMRRGRETL LTLLEAFVYD PLVDWTAGGE AGFAGAVYGG GGQQAESKQS KREMEREITR
  2461  SLFSSRVAEI KVNWFKNRDE MLVVLPKLDG SLDEYLSLQE QLTDVEKLQG KLLEEIEFLE
  2521  GAEGVDHPSH TLQHRYSEHT QLQTQQRAVQ EAIQVKLNEF EQWITHYQAA FNNLEATQLA
  2581  SLLQEISTQM DLGPPSYVPA TAFLQNAGQA HLISQCEQLE GEVGALLQQR RSVLRGCLEQ
  2641  LHHYATVALQ YPKAIFQKHR IEQWKTWMEE LICNTTVERC QELYRKYEMQ YAPQPPPTVC
  2701  QFITATEMTL QRYAADINSR LIRQVERLKQ EAVTVPVCED QLKEIERCIK VFLHENGEEG
  2761  SLSLASVIIS ALCTLTRRNL MMEGAASSAG EQLVDLTSRD GAWFLEELCS MSGNVTCLVQ
  2821  LLKQCHLVPQ DLDIPNPMEA SETVHLANGV YTSLQELNSN FRQIIFPEAL RCLMKGEYTL
  2881  ESMLHELDGL IEQTTDGVPL QTLVESLQAY LRNAAMGLEE ETHAHYIDVA RLLHAQYGEL
  2941  IQPRNGSVDE TPKMSAGQML LVAFDGMFAQ VETAFSLLVE KLNKMEIPIA WRKIDIIREA
  3001  RSTQVNFFDD DNHRQVLEEI FFLKRLQTIK EFFRLCGTFS KTLSGSSSLE DQNTVNGPVQ
  3061  IVNVKTLFRN SCFSEDQMAK PIKAFTADFV RQLLIGLPNQ ALGLTLCSFI SALGVDIIAQ
  3121  VEAKDFGAES KVSVDDLCKK AVEHNIQIGK FSQLVMNRAT VLASSYDTAW KKHDLVRRLE
  3181  TSISSCKTSL QRVQLHIAMF QWQHEDLLIN RPQAMSVTPP PRSAILTSMK KKLHTLSQIE
  3241  TSIATVQEKL AALESSIEQR LKWAGGANPA LAPVLQDFEA TIAERRNLVL KESQRASQVT
  3301  FLCSNIIHFE SLRTRTAEAL NLDAALFELI KRCQQMCSFA SQFNSSVSEL ELRLLQRVDT
  3361  GLEHPIGSSE WLLSAHKQLT QDMSTQRAIQ TEKEQQIETV CETIQNLVDN IKTVLTGHNR
  3421  QLGDVKHLLK AMAKDEEAAL ADGEDVPYEN SVRQFLGEYK SWQDNIQTVL FTLVQAMGQV
  3481  RSQEHVEMLQ EITPTLKELK TQSQSIYNNL VSFASPLVTD ATNECSSPTS SATYQPSFAA
  3541  AVRSNTGQKT QPDVMSQNAR KLIQKNLATS ADTPPSTVPG TGKSVACSPK KAVRDPKTGK
  3601  AVQERNSYAV SVWKRVKAKL EGRDVDPNRR MSVAEQVDYV IKEATNLDNL AQLYEGWTAW
  3661  V

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SMG1 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
Highest tissue expression: 50 nTPM

Expression across tissuesHPA

Tissue

skeletal muscle: 50 nTPM
skin: 40 nTPM
bone marrow: 39 nTPM
tongue: 34 nTPM
thymus: 29 nTPM
cerebellum: 26 nTPM

Single-cell type

thymic myoid cells: 611 nCPM
myonuclei: 463 nCPM
neutrophils: 411 nCPM
basal keratinocytes: 304 nCPM
neutrophil progenitors: 285 nCPM
cardiomyocytes: 267 nCPM

Immune cell

basophil: 35 nTPM
neutrophil: 11 nTPM
naive B-cell: 9.8 nTPM
gdT-cell: 8.9 nTPM
non-classical monocyte: 8.3 nTPM
naive CD4 T-cell: 7.5 nTPM

Brain region

cerebellum: 188 nTPM
white matter: 121 nTPM
amygdala: 114 nTPM
hypothalamus: 113 nTPM
thalamus: 112 nTPM
cerebral cortex: 111 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SMG1.

Disease | ImmuneIEDB

Conditions an epitope on SMG1 was assayed in.

collecting duct carcinoma T cell
type 1 diabetes mellitus T cell

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): 0.05
gnomAD pLI: 1
gnomAD missense Z: 3.3
DepMap mean gene effect: -1.09
DepMap dependency class: common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% 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

Phosphatidylinositol 3-/4-kinase, catalytic domain
FATC domain
Protein kinase-like domain superfamily
Armadillo-like helical
PIK-related kinase, FAT domain
Armadillo-type fold
Phosphatidylinositol 3-/4-kinase, conserved site
Serine/threonine-protein kinase SMG1, N-terminal
Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily
DNA Damage Response and Repair Kinase
Phosphatidylinositol 3- and 4-kinase
FATC domain
Serine/threonine-protein kinase SMG1 N-terminal
Serine/threonine-protein kinase SMG1
SMG1, PIKK catalytic domain
Serine/threonine-protein kinase smg-1

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SMG1 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 SMG1 as an antibody target. Whether an autoantibody or antibody against SMG1 could matter depends on whether native SMG1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SMG1 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 SMG1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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