Seroatlas · Human Serome Atlas

CHD3

Chromodomain-helicase-DNA-binding protein 3

Also known as: CHD3_HUMAN, Mi-2a, Mi2-ALPHA, ZFH

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

Protein identityUniProt · HPA

UniProt accession: Q12873
Gene: CHD3
Ensembl: ENSG00000170004
Chromosome: 17
Canonical length: 2000 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Plasma proteins, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Nucleoli,Centriolar satellite

OverviewNCBI Gene

This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

2000 residues, UniProt reviewed canonical sequence.

>Q12873|CHD3
     1  MKAADTVILW ARSKNDQLRI SFPPGLCWGD RMPDKDDIRL LPSALGVKKR KRGPKKQKEN
    61  KPGKPRKRKK RDSEEEFGSE RDEYREKSES GGSEYGTGPG RKRRRKHREK KEKKTKRRKK
   121  GEGDGGQKQV EQKSSATLLL TWGLEDVEHV FSEEDYHTLT NYKAFSQFMR PLIAKKNPKI
   181  PMSKMMTILG AKWREFSANN PFKGSAAAVA AAAAAAAAAV AEQVSAAVSS ATPIAPSGPP
   241  ALPPPPAADI QPPPIRRAKT KEGKGPGHKR RSKSPRVPDG RKKLRGKKMA PLKIKLGLLG
   301  GKRKKGGSYV FQSDEGPEPE AEESDLDSGS VHSASGRPDG PVRTKKLKRG RPGRKKKKVL
   361  GCPAVAGEEE VDGYETDHQD YCEVCQQGGE IILCDTCPRA YHLVCLDPEL DRAPEGKWSC
   421  PHCEKEGVQW EAKEEEEEYE EEGEEEGEKE EEDDHMEYCR VCKDGGELLC CDACISSYHI
   481  HCLNPPLPDI PNGEWLCPRC TCPVLKGRVQ KILHWRWGEP PVAVPAPQQA DGNPDVPPPR
   541  PLQGRSEREF FVKWVGLSYW HCSWAKELQL EIFHLVMYRN YQRKNDMDEP PPLDYGSGED
   601  DGKSDKRKVK DPHYAEMEEK YYRFGIKPEW MTVHRIINHS VDKKGNYHYL VKWRDLPYDQ
   661  STWEEDEMNI PEYEEHKQSY WRHRELIMGE DPAQPRKYKK KKKELQGDGP PSSPTNDPTV
   721  KYETQPRFIT ATGGTLHMYQ LEGLNWLRFS WAQGTDTILA DEMGLGKTIQ TIVFLYSLYK
   781  EGHTKGPFLV SAPLSTIINW EREFQMWAPK FYVVTYTGDK DSRAIIRENE FSFEDNAIKG
   841  GKKAFKMKRE AQVKFHVLLT SYELITIDQA ALGSIRWACL VVDEAHRLKN NQSKFFRVLN
   901  GYKIDHKLLL TGTPLQNNLE ELFHLLNFLT PERFNNLEGF LEEFADISKE DQIKKLHDLL
   961  GPHMLRRLKA DVFKNMPAKT ELIVRVELSP MQKKYYKYIL TRNFEALNSR GGGNQVSLLN
  1021  IMMDLKKCCN HPYLFPVAAM ESPKLPSGAY EGGALIKSSG KLMLLQKMLR KLKEQGHRVL
  1081  IFSQMTKMLD LLEDFLDYEG YKYERIDGGI TGALRQEAID RFNAPGAQQF CFLLSTRAGG
  1141  LGINLATADT VIIFDSDWNP HNDIQAFSRA HRIGQANKVM IYRFVTRASV EERITQVAKR
  1201  KMMLTHLVVR PGLGSKAGSM SKQELDDILK FGTEELFKDE NEGENKEEDS SVIHYDNEAI
  1261  ARLLDRNQDA TEDTDVQNMN EYLSSFKVAQ YVVREEDKIE EIEREIIKQE ENVDPDYWEK
  1321  LLRHHYEQQQ EDLARNLGKG KRVRKQVNYN DAAQEDQDNQ SEYSVGSEEE DEDFDERPEG
  1381  RRQSKRQLRN EKDKPLPPLL ARVGGNIEVL GFNTRQRKAF LNAVMRWGMP PQDAFTTQWL
  1441  VRDLRGKTEK EFKAYVSLFM RHLCEPGADG SETFADGVPR EGLSRQQVLT RIGVMSLVKK
  1501  KVQEFEHING RWSMPELMPD PSADSKRSSR ASSPTKTSPT TPEASATNSP CTSKPATPAP
  1561  SEKGEGIRTP LEKEEAENQE EKPEKNSRIG EKMETEADAP SPAPSLGERL EPRKIPLEDE
  1621  VPGVPGEMEP EPGYRGDREK SATESTPGER GEEKPLDGQE HRERPEGETG DLGKREDVKG
  1681  DRELRPGPRD EPRSNGRREE KTEKPRFMFN IADGGFTELH TLWQNEERAA ISSGKLNEIW
  1741  HRRHDYWLLA GIVLHGYARW QDIQNDAQFA IINEPFKTEA NKGNFLEMKN KFLARRFKLL
  1801  EQALVIEEQL RRAAYLNLSQ EPAHPAMALH ARFAEAECLA ESHQHLSKES LAGNKPANAV
  1861  LHKVLNQLEE LLSDMKADVT RLPATLSRIP PIAARLQMSE RSILSRLASK GTEPHPTPAY
  1921  PPGPYATPPG YGAAFSAAPV GALAAAGANY SQMPAGSFIT AATNGPPVLV KKEKEMVGAL
  1981  VSDGLDRKEP RAGEVICIDD

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CHD3 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): 0.44
Highest tissue expression: 66 nTPM

Expression across tissuesHPA

Tissue

cervix: 66 nTPM
prostate: 58 nTPM
endometrium: 56 nTPM
ovary: 53 nTPM
thymus: 53 nTPM
fallopian tube: 52 nTPM

Single-cell type

prostatic glandular cells: 185 nCPM
tuft cells: 150 nCPM
podocytes: 142 nCPM
prostatic club cells: 142 nCPM
prostatic hillock cells: 142 nCPM
salivary duct cells: 121 nCPM

Immune cell

naive CD4 T-cell: 4.4 nTPM
memory CD4 T-cell: 4.1 nTPM
memory CD8 T-cell: 3.9 nTPM
gdT-cell: 3.8 nTPM
MAIT T-cell: 3.4 nTPM
eosinophil: 3.3 nTPM

Brain region

cerebral cortex: 149 nTPM
hippocampal formation: 128 nTPM
basal ganglia: 123 nTPM
white matter: 110 nTPM
amygdala: 101 nTPM
hypothalamus: 82 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CHD3.

Disease | AllUniProt

Conditions CHD3 is implicated in, by any mechanism.

Snijders Blok-Campeau syndrome (SNIBCPS) MIM:618205

Disease | GeneticClinVar

124 pathogenic / likely-pathogenic of 848 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Snijders Blok-Campeau syndrome
Inborn genetic diseases
Intellectual disability
CHD3-related disorder
Neurodevelopmental abnormality

Disease | ImmuneIEDB

Conditions an epitope on CHD3 was assayed in.

hepatocellular carcinoma 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): 0.15
gnomAD pLI: 1
gnomAD missense Z: 6.15
DepMap mean gene effect: -0.02
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% 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 CHD3 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 CHD3 as an antibody target. Whether an autoantibody or antibody against CHD3 could matter depends on whether native CHD3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CHD3 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.

Source-annotated serology context

The source annotations explicitly mention antibody, autoantibody, autoantigen, or autoimmune context. This is biological context, not study-specific reactivity.

Autoantibodies against this protein are found in a subset of patients with dermatomyositis.

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