ZNF630

gene
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Also known as BC037316dJ54B20.2FLJ20573MGC138344

Summary

ZNF630 (zinc finger protein 630, HGNC:28855) is a protein-coding gene on chromosome Xp11.23, encoding Zinc finger protein 630 (Q2M218). May be involved in transcriptional regulation.

This gene encodes a protein containing an N-terminal Kruppel-associated box-containing (KRAB) domain and 13 Kruppel-type C2H2 zinc finger domains. This gene resides on an area of chromosome X that has been implicated in nonsyndromic X-linked cognitive disability. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 57232 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 79 total
  • MANE Select transcript: NM_001282201

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28855
Approved symbolZNF630
Namezinc finger protein 630
LocationXp11.23
Locus typegene with protein product
StatusApproved
AliasesBC037316, dJ54B20.2, FLJ20573, MGC138344
Ensembl geneENSG00000221994
Ensembl biotypeprotein_coding
OMIM300819
Entrez57232

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 nonsense_mediated_decay

ENST00000276054, ENST00000409324, ENST00000421903, ENST00000428463, ENST00000428686, ENST00000442455, ENST00000616492, ENST00000627643, ENST00000871921, ENST00000951017, ENST00000951018

RefSeq mRNA: 4 — MANE Select: NM_001282201 NM_001037735, NM_001190255, NM_001282201, NM_001282202

CCDS: CCDS35237

Canonical transcript exons

ENST00000276054 — 5 exons

ExonStartEnd
ENSE000036631584806081948060945
ENSE000036807684806045048060545
ENSE000038965394806687248067061
ENSE000038968014807126748071640
ENSE000038969334805751648060203

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 78.93.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4793 / max 26.2194, expressed in 832 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1991491.4793832

Top tissues by expression

239 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cardiac muscle of right atriumUBERON:000337978.93gold quality
left ventricle myocardiumUBERON:000656678.90gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099176.79silver quality
upper arm skinUBERON:000426374.19gold quality
islet of LangerhansUBERON:000000673.82gold quality
cortical plateUBERON:000534373.74gold quality
kidney epitheliumUBERON:000481973.66gold quality
left ovaryUBERON:000211973.49gold quality
thoracic aortaUBERON:000151572.72gold quality
lower esophagus mucosaUBERON:003583472.72gold quality
ascending aortaUBERON:000149672.69gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047372.59gold quality
descending thoracic aortaUBERON:000234572.58gold quality
endocervixUBERON:000045872.53gold quality
colonic epitheliumUBERON:000039772.29gold quality
right ovaryUBERON:000211872.10gold quality
smooth muscle tissueUBERON:000113572.09gold quality
aortaUBERON:000094772.00gold quality
right coronary arteryUBERON:000162571.77gold quality
cerebellar hemisphereUBERON:000224571.57gold quality
popliteal arteryUBERON:000225071.57gold quality
cerebellar cortexUBERON:000212971.55gold quality
tibial arteryUBERON:000761071.55gold quality
cardiac atriumUBERON:000208171.35gold quality
ganglionic eminenceUBERON:000402371.23gold quality
right lobe of thyroid glandUBERON:000111971.22gold quality
right atrium auricular regionUBERON:000663171.09gold quality
left coronary arteryUBERON:000162671.04gold quality
thyroid glandUBERON:000204670.97gold quality
ectocervixUBERON:001224970.95gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-CURD-10no228.45
E-ANND-3no5.33

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

23 targeting ZNF630, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-139-5P99.8069.501399
HSA-MIR-442299.7272.072908
HSA-MIR-4524A-3P99.7266.852406
HSA-MIR-472999.6972.184233
HSA-MIR-320299.6667.702737
HSA-MIR-26A-1-3P99.6466.81788
HSA-MIR-26A-2-3P99.6466.82786
HSA-MIR-58799.6470.862611
HSA-MIR-653-5P99.4667.351300
HSA-MIR-488-5P99.2868.12821
HSA-MIR-472199.2666.05818
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-6731-3P98.6167.86749
HSA-MIR-7114-5P98.5167.871349
HSA-MIR-6804-5P98.3965.771084
HSA-MIR-4778-5P97.9668.061634
HSA-MIR-204-3P97.8066.841656
HSA-MIR-4646-5P97.7066.841692
HSA-MIR-3928-3P97.6166.531096
HSA-MIR-431497.5067.301369
HSA-MIR-96-3P97.4768.03839

Literature-anchored findings (GeneRIF, showing 1)

  • Detected 12 ZNF630 deletions in a total of 1,562 male patients with mental retardation from Brazil, USA, Australia, and Europe. The breakpoints were analyzed in 10 families, and in all cases they were located within two segmental duplications. (PMID:20186789)

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 630Q2M218 (reviewed: Q2M218)

All UniProt accessions (7): Q2M218, A0A087WXA8, A0A0D9SER6, A0A6E1WMD9, B2ZWG8, B2ZWG9, F8WCH7

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt IDNamesCanonical?
Q2M218-11yes
Q2M218-22

RefSeq proteins (4): NP_001032824, NP_001177184, NP_001269130, NP_001269131 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001909KRABDomain
IPR013087Znf_C2H2_typeDomain
IPR036051KRAB_dom_sfHomologous_superfamily
IPR036236Znf_C2H2_sfHomologous_superfamily

Pfam: PF00096, PF01352

UniProt features (18 total): zinc finger region 14, chain 1, domain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q2M218-F167.640.13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): CAMPS_COLON_CANCER_COPY_NUMBER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chrXp11, ZWANG_DOWN_BY_2ND_EGF_PULSE, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR4422, MIR4524A_3P, MIR139_5P, MIR3928_3P, MIR26A_1_3P, MIR26A_2_3P, GSE14000_UNSTIM_VS_4H_LPS_DC_UP, GSE14000_4H_VS_16H_LPS_DC_DN, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_DN, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nuclear lumen (GO:0031981)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
cis-regulatory region sequence-specific DNA binding1
chromatin1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
transition metal ion binding1
nucleic acid binding1
cation binding1
intracellular membrane-bounded organelle1
nucleus1
intracellular organelle lumen1

Protein interactions and networks

STRING

272 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZNF630SPACA5BQ96QH8627
ZNF630ITIH6Q6UXX5447
ZNF630CFAP47Q6ZTR5447
ZNF630EOLA1Q8TE69447
ZNF630OR6C6A6NF89433
ZNF630CCDC59Q9P031418
ZNF630INTS6LQ5JSJ4401
ZNF630TMEM185AQ8NFB2379
ZNF630OR6C65A6NJZ3370
ZNF630SSX3Q99909352
ZNF630CCDC85BQ15834311
ZNF630ASB9Q96DX5310
ZNF630POGZQ7Z3K3306
ZNF630TSEN54Q7Z6J9306
ZNF630MAGEA9BP43362302

IntAct

2 interactions, top by confidence:

ABTypeScore
GPC3PXDNLpsi-mi:“MI:0914”(association)0.350

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0JPK3, A8MT65, C9JN71, E9QAG8, G3X9G7, O75820, P16373, P16374, P16415, P17017, P17024, P17025, P51815, P52737, Q08AG5, Q08ER8, Q0D2J5, Q15973, Q2M218, Q3KP31, Q3V080, Q494X3, Q4R4C7, Q5MYW4, Q5R9F0, Q5R9S5, Q5REI6, Q5REK1, Q68EA5, Q6P560, Q6P5C7, Q6ZQV5, Q7L945, Q86T29, Q8BGV5, Q8C6P8, Q8IYI8, Q8IZC7, Q8N7K0, Q8N972

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

79 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1573 predictions. Top by Δscore:

VariantEffectΔscore
X:48008532:ATGG:Adonor_loss1.0000
X:48008534:GGT:Gdonor_loss1.0000
X:48008535:G:Cdonor_loss1.0000
X:48008536:T:Adonor_loss1.0000
X:48071341:C:Adonor_gain1.0000
X:48071345:T:TAdonor_gain1.0000
X:48071353:T:TAdonor_gain1.0000
X:48071354:C:Adonor_gain1.0000
X:47983408:GCCCC:Gacceptor_loss0.9900
X:47983411:CCTG:Cacceptor_loss0.9900
X:47983412:C:Aacceptor_loss0.9900
X:47983413:T:Aacceptor_loss0.9900
X:47988520:ATACC:Adonor_loss0.9900
X:47988521:TACCT:Tdonor_loss0.9900
X:47988522:ACCTG:Adonor_loss0.9900
X:47988523:C:CGdonor_loss0.9900
X:48008375:GGGCT:Gacceptor_gain0.9900
X:48008530:TCATG:Tdonor_gain0.9900
X:48008533:TG:Tdonor_gain0.9900
X:48008534:GG:Gdonor_gain0.9900
X:48008535:G:GGdonor_gain0.9900
X:48009362:TCA:Tacceptor_loss0.9900
X:48009364:A:AGacceptor_gain0.9900
X:48009364:AGAC:Aacceptor_loss0.9900
X:48009365:G:GAacceptor_gain0.9900
X:48009365:GAC:Gacceptor_gain0.9900
X:48009365:GACCT:Gacceptor_gain0.9900
X:48060542:CACC:Cacceptor_gain0.9900
X:48060544:CC:Cacceptor_gain0.9900
X:48060545:CC:Cacceptor_gain0.9900

AlphaMissense

3558 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:48058786:A:CF552L0.995
X:48058786:A:TF552L0.995
X:48058788:A:GF552L0.995
X:48058954:G:CF496L0.995
X:48058954:G:TF496L0.995
X:48058956:A:GF496L0.995
X:48059038:A:CF468L0.994
X:48059038:A:TF468L0.994
X:48059040:A:GF468L0.994
X:48058870:G:CF524L0.993
X:48058870:G:TF524L0.993
X:48058872:A:GF524L0.993
X:48058769:A:GL558P0.991
X:48059122:G:CF440L0.991
X:48059122:G:TF440L0.991
X:48059124:A:GF440L0.991
X:48058757:T:GQ562P0.990
X:48058925:T:GQ506P0.990
X:48058853:A:GL530P0.989
X:48059021:A:GL474P0.989
X:48058937:A:GL502P0.988
X:48058915:A:CH509Q0.987
X:48058915:A:TH509Q0.987
X:48059290:G:CF384L0.987
X:48059290:G:TF384L0.987
X:48059292:A:GF384L0.987
X:48059374:G:CF356L0.987
X:48059374:G:TF356L0.987
X:48059376:A:GF356L0.987
X:48058702:G:CF580L0.986

dbSNP variants (sampled 300 via entrez): RS1000187500 (X:48070859 G>A,C), RS1000455425 (X:48062654 A>T), RS1000727379 (X:48070335 G>A,C,T), RS1001189150 (X:48072707 G>T), RS1001467389 (X:48064555 C>T), RS1001772490 (X:48064791 G>A,C), RS1002430636 (X:48066147 T>C), RS1002871999 (X:48066649 T>C), RS1003357672 (X:48059414 C>G), RS1003932265 (X:48062272 A>G), RS1004442525 (X:48069560 G>A), RS1004898191 (X:48063694 C>A), RS1004929222 (X:48064010 G>C,T), RS1005505000 (X:48071751 C>G), RS1005845700 (X:48071488 G>A,C)

Disease associations

OMIM: gene MIM:300819 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary ovarian failure (MONDO:0005387)

Orphanet (1): NON RARE IN EUROPE: Primary ovarian failure (Orphanet:619)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D016649Primary Ovarian InsufficiencyC12.050.351.500.056.630.750; C12.100.250.056.630.750; C19.391.630.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
Valproic Aciddecreases expression2
FR900359increases phosphorylation1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
CGP 52608affects binding, increases reaction1
tanespimycinincreases expression, affects cotreatment1
abrineincreases expression1
5-(2,4-dihydroxy-5-isopropylphenyl)-4-(4-morpholin-4-ylmethylphenyl)isoxazole-3-carboxylic acid ethylamideincreases expression1
STA 9090increases expression1
VER 155008affects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Benzo(a)pyreneincreases methylation1
Silicon Dioxidedecreases expression1
Tetrachlorodibenzodioxinaffects expression1

Clinical trials (associated diseases)

75 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00417066PHASE4COMPLETEDFlexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693PHASE4COMPLETEDEvaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616PHASE4COMPLETEDEstrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501PHASE4UNKNOWNEffects of ADSC Therapy in Women With POF
NCT02783937PHASE4COMPLETEDFilgrastim for Premature Ovarian Insufficiency
NCT03535480PHASE4UNKNOWNAutologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00140998PHASE3COMPLETEDEstrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00001951PHASE2COMPLETEDHormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019PHASE2WITHDRAWNEffects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494PHASE2COMPLETEDGnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852PHASE2SUSPENDEDThe Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467PHASE2UNKNOWNPrevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982PHASE2COMPLETEDThe Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT02912104PHASE1COMPLETEDA Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695PHASE1COMPLETEDInovium Ovarian Rejuvenation Trials
NCT04815213PHASE1ACTIVE_NOT_RECRUITINGThe Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367PHASE1COMPLETEDEffects of UCA-PSCs in Women With POF
NCT06132542PHASE1UNKNOWNAutologous ADMSC Transplantation in Patients With POI
NCT00948857PHASE2/PHASE3TERMINATEDDehydroepiandrosterone (DHEA) Treatment and Premature Ovarian Failure (POF)
NCT04031456PHASE2/PHASE3RECRUITINGAutologous PRP Infusion May Restore Ovarian Function and May Promote Folliculogenesis in POI Patients
NCT02043743PHASE1/PHASE2UNKNOWNAutologous Stem Cells Transplantation in Patients With Idiopathic and Drug Induced Premature Ovarian Failure
NCT02062931PHASE1/PHASE2UNKNOWNAutologous Mesenchymal Stem Cells Transplantation In Women With Premature Ovarian Failure
NCT02151890PHASE1/PHASE2COMPLETEDPregnancy After Stem Cell Transplantation in Premature Ovarian Failure
NCT02372474PHASE1/PHASE2COMPLETEDIt is a Real The First Baby Of Autologous Stem Cell Therapy in Premature Ovarian Failure
NCT02603744PHASE1/PHASE2UNKNOWNAutologous Adipose Derived Mesenchymal Stromal Cells Transplantation in Women With Premature Ovarian Failure (POF)
NCT02644447PHASE1/PHASE2COMPLETEDTransplantation of HUC-MSCs With Injectable Collagen Scaffold for POF
NCT03069209PHASE1/PHASE2UNKNOWNAutologous Bone Marrow-Derived Stem Cell Transplantation in Patients With Premature Ovarian Failure (POF)
NCT03985462PHASE1/PHASE2WITHDRAWNVery Small Embryonic-like Stem Cells for Ovary
NCT04009473PHASE1/PHASE2UNKNOWNStem Cell Therapy and Growth Factor Ovarian in Vitro Activation
NCT04071574PHASE1/PHASE2COMPLETEDComparative Study on the Efficacy of Ovarian Stimulation Protocols on the Success Rate of ICSI in Female Infertility
NCT04922398PHASE1/PHASE2UNKNOWNOvarian Injection of PRP (Platelet -Rich Plasma) Vs Normal Saline in Premature Ovarian Insufficiency
NCT05462379PHASE1/PHASE2ACTIVE_NOT_RECRUITINGAutologous Heterotopic Fresh Ovarian Graft in Woman With LACC Eligible for Pelvic Radiotherapy Treatment.
NCT06202547PHASE1/PHASE2UNKNOWNIntra-ovarian Injection of MSC-EVs in Idiopathic Premature Ovarian Failure
NCT01129947EARLY_PHASE1WITHDRAWNThe Use of DHEA in Women With Premature Ovarian Failure
NCT05522634EARLY_PHASE1UNKNOWNA Clinical Study of Chinese Herbal Compound TJAOA101 in the Treatment of Premature Ovarian Insufficiency
NCT07308327EARLY_PHASE1ACTIVE_NOT_RECRUITINGThe Influence of Gut Microbiota on Ovarian Function: A Single-center, Randomized,Double Blind, Parallel-controlled, Exploratory Clinical Trial
NCT00001275Not specifiedCOMPLETEDOvarian Follicle Function in Patients With Primary Ovarian Failure
NCT00001306Not specifiedCOMPLETEDSteroid Therapy in Autoimmune Premature Ovarian Failure
NCT00006156Not specifiedCOMPLETEDFeasibility Study for Development of an Early Test for Ovarian Failure
NCT00119925Not specifiedUNKNOWN‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.