Seroatlas · Human Serome Atlas

SETD1A

Histone-lysine N-methyltransferase SETD1A

Also known as: KIAA0339, KMT2F, Set1, SET1A, SET1A_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
O15047
Gene
SETD1A
Ensembl
ENSG00000099381
Chromosome
16
Canonical length
1707 aa
Protein class
Disease related genes, Enzymes, Human disease related genes, Metabolic proteins, Potential drug targets, Predicted intracellular proteins
Subcellular location
Nuclear speckles
Quaternary structure
Homotrimer

OverviewNCBI Gene

The protein encoded by this gene is a component of a histone methyltransferase (HMT) complex that produces mono-, di-, and trimethylated histone H3 at Lys4. Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to generally mark the transcription start sites of active genes. The protein contains SET domains, a RNA recognition motif domain and is a member of the class V-like SAM-binding methyltransferase superfamily. [provided by RefSeq, Dec 2016]

Canonical amino-acid sequenceUniProt

1707 residues, UniProt reviewed canonical sequence.

>O15047|SETD1A
     1  MDQEGGGDGQ KAPSFQWRNY KLIVDPALDP ALRRPSQKVY RYDGVHFSVN DSKYIPVEDL
    61  QDPRCHVRSK NRDFSLPVPK FKLDEFYIGQ IPLKEVTFAR LNDNVRETFL KDMCRKYGEV
   121  EEVEILLHPR TRKHLGLARV LFTSTRGAKE TVKNLHLTSV MGNIIHAQLD IKGQQRMKYY
   181  ELIVNGSYTP QTVPTGGKAL SEKFQGSGAA TETAESRRRS SSDTAAYPAG TTAVGTPGNG
   241  TPCSQDTSFS SSRQDTPSSF GQFTPQSSQG TPYTSRGSTP YSQDSAYSSS TTSTSFKPRR
   301  SENSYQDAFS RRHFSASSAS TTASTAIAAT TAATASSSAS SSSLSSSSSS SSSSSSSQFR
   361  SSDANYPAYY ESWNRYQRHT SYPPRRATRE EPPGAPFAEN TAERFPPSYT SYLPPEPSRP
   421  TDQDYRPPAS EAPPPEPPEP GGGGGGGGPS PEREEVRTSP RPASPARSGS PAPETTNESV
   481  PFAQHSSLDS RIEMLLKEQR SKFSFLASDT EEEEENSSMV LGARDTGSEV PSGSGHGPCT
   541  PPPAPANFED VAPTGSGEPG ATRESPKANG QNQASPCSSG DDMEISDDDR GGSPPPAPTP
   601  PQQPPPPPPP PPPPPPYLAS LPLGYPPHQP AYLLPPRPDG PPPPEYPPPP PPPPHIYDFV
   661  NSLELMDRLG AQWGGMPMSF QMQTQMLTRL HQLRQGKGLI AASAGPPGGA FGEAFLPFPP
   721  PQEAAYGLPY ALYAQGQEGR GAYSREAYHL PMPMAAEPLP SSSVSGEEAR LPPREEAELA
   781  EGKTLPTAGT VGRVLAMLVQ EMKSIMQRDL NRKMVENVAF GAFDQWWESK EEKAKPFQNA
   841  AKQQAKEEDK EKTKLKEPGL LSLVDWAKSG GTTGIEAFAF GSGLRGALRL PSFKVKRKEP
   901  SEISEASEEK RPRPSTPAEE DEDDPEQEKE AGEPGRPGTK PPKRDEERGK TQGKHRKSFA
   961  LDSEGEEASQ ESSSEKDEED DEEDEEDEDR EEAVDTTKKE TEVSDGEDEE SDSSSKCSLY
  1021  ADSDGENDST SDSESSSSSS SSSSSSSSSS SSSSSSSSES SSEDEEEEER PAALPSASPP
  1081  PREVPVPTPA PVEVPVPERV AGSPVTPLPE QEASPARPAG PTEESPPSAP LRPPEPPAGP
  1141  PAPAPRPDER PSSPIPLLPP PKKRRKTVSF SAIEVVPAPE PPPATPPQAK FPGPASRKAP
  1201  RGVERTIRNL PLDHASLVKS WPEEVSRGGR SRAGGRGRLT EEEEAEPGTE VDLAVLADLA
  1261  LTPARRGLPA LPAVEDSEAT ETSDEAERPR PLLSHILLEH NYALAVKPTP PAPALRPPEP
  1321  VPAPAALFSS PADEVLEAPE VVVAEAEEPK PQQLQQQREE GEEEGEEEGE EEEEESSDSS
  1381  SSSDGEGALR RRSLRSHARR RRPPPPPPPP PPRAYEPRSE FEQMTILYDI WNSGLDSEDM
  1441  SYLRLTYERL LQQTSGADWL NDTHWVHHTI TNLTTPKRKR RPQDGPREHQ TGSARSEGYY
  1501  PISKKEKDKY LDVCPVSARQ LEGVDTQGTN RVLSERRSEQ RRLLSAIGTS AIMDSDLLKL
  1561  NQLKFRKKKL RFGRSRIHEW GLFAMEPIAA DEMVIEYVGQ NIRQMVADMR EKRYVQEGIG
  1621  SSYLFRVDHD TIIDATKCGN LARFINHCCT PNCYAKVITI ESQKKIVIYS KQPIGVDEEI
  1681  TYDYKFPLED NKIPCLCGTE SCRGSLN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SETD1A 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)
0.6
Highest tissue expression
20 nTPM

Expression across tissuesHPA

Tissue

  • bone marrow: 20 nTPM
  • testis: 13 nTPM
  • skeletal muscle: 11 nTPM
  • thymus: 9.6 nTPM
  • lymph node: 9.3 nTPM
  • pancreas: 9.3 nTPM

Single-cell type

  • undifferentiated spermatogonia: 33 nCPM
  • erythrocyte progenitors: 31 nCPM
  • differentiating spermatogonia: 24 nCPM
  • early primary spermatocytes: 22 nCPM
  • adrenal medulla cells: 21 nCPM
  • retinal horizontal cells: 20 nCPM

Immune cell

  • eosinophil: 0.7 nTPM
  • plasmacytoid DC: 0.6 nTPM
  • MAIT T-cell: 0.5 nTPM
  • naive B-cell: 0.5 nTPM
  • gdT-cell: 0.3 nTPM
  • intermediate monocyte: 0.3 nTPM

Brain region

  • cerebellum: 25 nTPM
  • cerebral cortex: 24 nTPM
  • thalamus: 20 nTPM
  • white matter: 20 nTPM
  • amygdala: 20 nTPM
  • medulla oblongata: 19 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SETD1A.

Disease | AllUniProt

Conditions SETD1A is implicated in, by any mechanism.

  • Epilepsy, early-onset, 2, with or without developmental delay (EPEO2) MIM:618832
  • Neurodevelopmental disorder with speech impairment and dysmorphic facies (NEDSID) MIM:619056

Disease | GeneticClinVar

71 pathogenic / likely-pathogenic of 816 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • Neurodevelopmental disorder with speech impairment and dysmorphic facies
  • Epilepsy, early-onset, with or without developmental delay
  • Inborn genetic diseases
  • Schizophrenia
  • SETD1A-related disorder

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)
0.14
gnomAD pLI
1
gnomAD missense Z
1.83
DepMap mean gene effect
-0.8
DepMap dependency class
common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SETD1A 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 SETD1A as an antibody target. Whether an autoantibody or antibody against SETD1A could matter depends on whether native SETD1A is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SETD1A 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 SETD1A as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/SETD1A. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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