GSC2

gene
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Summary

GSC2 (goosecoid homeobox 2, HGNC:4613) is a protein-coding gene on chromosome 22q11.21, encoding Homeobox protein goosecoid-2 (O15499). May have a role in development.

Goosecoidlike (GSCL), a homeodomain-containing gene, resides in the critical region for VCFS/DGS on 22q11. Velocardiofacial syndrome (VCFS) is a developmental disorder characterized by conotruncal heart defects, craniofacial anomalies, and learning disabilities. VCFS is phenotypically related to DiGeorge syndrome (DGS) and both syndromes are associated with hemizygous 22q11 deletions. Because many of the tissues and structures affected in VCFS/DGS derive from the pharyngeal arches of the developing embryo, it is believed that haploinsufficiency of a gene involved in embryonic development may be responsible for its etiology. The gene is expressed in a limited number of adult tissues, as well as in early human development.

Source: NCBI Gene 2928 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 59 total — 4 pathogenic
  • MANE Select transcript: NM_005315

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4613
Approved symbolGSC2
Namegoosecoid homeobox 2
Location22q11.21
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000063515
Ensembl biotypeprotein_coding
OMIM601845
Entrez2928

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000086933

RefSeq mRNA: 1 — MANE Select: NM_005315 NM_005315

CCDS: CCDS13757

Canonical transcript exons

ENST00000086933 — 3 exons

ExonStartEnd
ENSE000003311061914699319149095
ENSE000006506511914966319149916
ENSE000006506521915002519150292

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 85.43.

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.43gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.68gold quality
testisUBERON:000047361.73gold quality
right testisUBERON:000453460.96gold quality
left testisUBERON:000453360.23gold quality
cortical plateUBERON:000534344.05silver quality
colonic epitheliumUBERON:000039741.17gold quality
sural nerveUBERON:001548840.94gold quality
bone marrow cellCL:000209239.99gold quality
lower esophagus mucosaUBERON:003583437.17gold quality
prefrontal cortexUBERON:000045137.05gold quality
bone marrowUBERON:000237136.95gold quality
apex of heartUBERON:000209836.51gold quality
ventricular zoneUBERON:000305336.48gold quality
granulocyteCL:000009436.03gold quality
ganglionic eminenceUBERON:000402335.49gold quality
skeletal muscle tissueUBERON:000113434.93gold quality
skin of legUBERON:000151134.91silver quality
zone of skinUBERON:000001434.40silver quality
skin of abdomenUBERON:000141633.44silver quality
ectocervixUBERON:001224933.31gold quality
frontal cortexUBERON:000187032.94gold quality
primary visual cortexUBERON:000243632.83gold quality
uterine cervixUBERON:000000232.68gold quality
superior frontal gyrusUBERON:000266132.35gold quality
muscle tissueUBERON:000238532.20gold quality
hindlimb stylopod muscleUBERON:000425232.15gold quality
leukocyteCL:000073831.90gold quality
nucleus accumbensUBERON:000188231.27gold quality
monocyteCL:000057630.52gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.20

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

TargetRegulation
GSC2
TH

JASPAR motifs

MotifNameFamily
MA0891.1GSC2Paired-related HD factors
MA0891.2GSC2Paired-related HD factors

JASPAR matrix evidence (PMIDs): PMID:9441739

Upstream regulators (CollecTRI, top): GSC2, GSC

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusGsc2ENSMUSG00000022738
rattus_norvegicusGsc2ENSRNOG00000000282

Paralogs (50): ARX (ENSG00000004848), PAX6 (ENSG00000007372), PAX7 (ENSG00000009709), ALX4 (ENSG00000052850), PITX1 (ENSG00000069011), PAX2 (ENSG00000075891), RHOXF1 (ENSG00000101883), CRX (ENSG00000105392), EVX1 (ENSG00000106038), PAX4 (ENSG00000106331), NOBOX (ENSG00000106410), PITX3 (ENSG00000107859), PHOX2B (ENSG00000109132), OTX1 (ENSG00000115507), PRRX1 (ENSG00000116132), VSX2 (ENSG00000119614), ESX1 (ENSG00000123576), PAX8 (ENSG00000125618), PAX1 (ENSG00000125813), RHOXF2 (ENSG00000131721), GSC (ENSG00000133937), RAX (ENSG00000134438), PAX3 (ENSG00000135903), ALX3 (ENSG00000156150), HESX1 (ENSG00000163666), PITX2 (ENSG00000164093), UNCX (ENSG00000164853), PHOX2A (ENSG00000165462), OTX2 (ENSG00000165588), DRGX (ENSG00000165606), PRRX2 (ENSG00000167157), SHOX2 (ENSG00000168779), OTP (ENSG00000171540), RAX2 (ENSG00000173976), EVX2 (ENSG00000174279), PROP1 (ENSG00000175325), ISX (ENSG00000175329), ALX1 (ENSG00000180318), MIXL1 (ENSG00000185155), SHOX (ENSG00000185960)

Protein

Protein identifiers

Homeobox protein goosecoid-2O15499 (reviewed: O15499)

Alternative names: Homeobox protein goosecoid-like

All UniProt accessions (1): O15499

UniProt curated annotations — full annotation on UniProt →

Function. May have a role in development. May regulate its own transcription. May bind the bicoid consensus sequence TAATCC.

Subcellular location. Nucleus.

Tissue specificity. Detected in adult testis and pituitary, and in 9-10 week fetal tissue (thorax). Probably expressed in other tissues at low levels.

Similarity. Belongs to the paired homeobox family. Bicoid subfamily.

RefSeq proteins (1): NP_005306* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR051440Goosecoid-like_HBFamily

Pfam: PF00046

UniProt features (5 total): region of interest 2, chain 1, DNA-binding region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15499-F170.080.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): BENPORATH_ES_WITH_H3K27ME3, HU_ANGIOGENESIS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, P53_DN.V2_UP, PRC2_EED_DN.V1_UP, GSE13522_WT_VS_IFNG_KO_SKIN_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, GSE14386_UNTREATED_VS_IFNA_TREATED_ACT_PBMC_MS_PATIENT_UP, GSE10325_BCELL_VS_LUPUS_BCELL_UP, GSE13306_RA_VS_UNTREATED_TREG_DN, GSE14769_20MIN_VS_360MIN_LPS_BMDM_DN, GSE14769_40MIN_VS_360MIN_LPS_BMDM_DN, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_UP, WP_22Q112_COPY_NUMBER_VARIATION_SYNDROME, MYOCD_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), anatomical structure morphogenesis (GO:0009653), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), sequence-specific DNA binding (GO:0043565), sequence-specific double-stranded DNA binding (GO:1990837), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
transcription by RNA polymerase II1
developmental process1
anatomical structure development1
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
nucleic acid binding1
transcription cis-regulatory region binding1
transcription regulator activity1
DNA binding1
double-stranded DNA binding1
sequence-specific DNA binding1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

348 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GSC2GNB1LQ9BYB4803
GSC2SLC25A1P53007780
GSC2TBX1O43435721
GSC2PRODHO43272714
GSC2PRODHO43272693
GSC2SEPTIN5Q99719674
GSC2GP1BBP13224671
GSC2RANBP1P43487640
GSC2DGCR2P98153630
GSC2CLTCL1P53675626
GSC2DGCR6LQ9BY27596
GSC2CLDN5O00501562
GSC2COMTP21964562
GSC2ZNF74Q16587560
GSC2DGCR6Q14129557

IntAct

173 interactions, top by confidence:

ABTypeScore
GSC2GTF2H5psi-mi:“MI:0915”(physical association)0.560
GSC2ASPHpsi-mi:“MI:0915”(physical association)0.560
SDCBPGSC2psi-mi:“MI:0915”(physical association)0.560
GSC2GUCY1A2psi-mi:“MI:0915”(physical association)0.560
GSC2BNIP2psi-mi:“MI:0915”(physical association)0.560
GSC2COL8A1psi-mi:“MI:0915”(physical association)0.560
GSC2psi-mi:“MI:0915”(physical association)0.560
GSC2CIAO2Apsi-mi:“MI:0915”(physical association)0.560
GSC2MAPK9psi-mi:“MI:0915”(physical association)0.560
GSC2MRPS23psi-mi:“MI:0915”(physical association)0.560
GSC2ANXA5psi-mi:“MI:0915”(physical association)0.560
GSC2EGLN3psi-mi:“MI:0915”(physical association)0.560
GSC2GALNT11psi-mi:“MI:0915”(physical association)0.560
GSC2PDE4Cpsi-mi:“MI:0915”(physical association)0.560
GSC2GUCA1Apsi-mi:“MI:0915”(physical association)0.560
GSC2PRKAB2psi-mi:“MI:0915”(physical association)0.560
GSC2KLHL38psi-mi:“MI:0915”(physical association)0.560
GSC2GCM2psi-mi:“MI:0915”(physical association)0.560
GSC2FKBP6psi-mi:“MI:0915”(physical association)0.560
GSC2ETFDHpsi-mi:“MI:0915”(physical association)0.560
TNPO2GSC2psi-mi:“MI:0915”(physical association)0.560
GSC2CRCPpsi-mi:“MI:0915”(physical association)0.560
GSC2CSNK2A1psi-mi:“MI:0915”(physical association)0.560
GSC2CDKN2Dpsi-mi:“MI:0915”(physical association)0.560
GSC2MORF4L1psi-mi:“MI:0915”(physical association)0.560
GSC2PTERpsi-mi:“MI:0915”(physical association)0.560
GSC2KRTAP5-9psi-mi:“MI:0915”(physical association)0.560
FAM221BGSC2psi-mi:“MI:0915”(physical association)0.560
GSC2CALRpsi-mi:“MI:0915”(physical association)0.560
GSC2LTO1psi-mi:“MI:0915”(physical association)0.560

BioGRID (61): GSC2 (Two-hybrid), GSC2 (Two-hybrid), TIPIN (Two-hybrid), FKBP6 (Two-hybrid), MID2 (Two-hybrid), PACSIN2 (Two-hybrid), CSNK2A1 (Two-hybrid), DYRK1B (Two-hybrid), TNPO2 (Two-hybrid), PDE4C (Two-hybrid), UBE2R2 (Two-hybrid), MAD2L2 (Two-hybrid), YPEL5 (Two-hybrid), GTSF1L (Two-hybrid), GCM2 (Two-hybrid)

ESM2 similar proteins: A0A0U1RQS6, A0A286YF58, A0A494C0N9, A0A494C0Y3, A0A7I2V3R4, A2AEV7, A2VDX9, A5PJP1, A6NCS6, A6NIN4, A6NJG2, A6NLJ0, A8MVW0, B7Z1M9, B8ZZ34, C9JTQ0, M0QZC1, O15499, O43541, P03971, P08353, P0C7L8, P0CG09, P0DPE3, P28283, P36313, P37318, P37319, Q0PHV7, Q1HCM0, Q29RM6, Q2EGB9, Q2KJ18, Q2M3V2, Q5VY09, Q6ZW31, Q8BLS7, Q8BRJ4, Q8N4B5, Q8NCU7

Diamond homologs: A0A1W2PPK0, A0A1W2PPM1, A1A546, A1YEY5, A1YFI3, A1YG57, A1YGA2, A2T733, A2T777, A2T7P4, A6NFQ7, G5EC89, L8E946, O14813, O15499, O35690, O42250, O42356, O42357, O42477, O70137, O73917, O75360, O95076, O97670, P0DMV5, P26367, P26630, P29454, P41935, P47237, P47238, P53544, P53545, P53546, P54366, P55813, P55864, P56915, P56916

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic0
Uncertain significance53
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1180540GRCh37/hg19 22q11.21(chr22:18889571-21464697)x1Pathogenic
1879566GRCh37/hg19 22q11.21(chr22:18893888-21570386)x1Pathogenic
526039NC_000022.10:g.(?18910310)(19770565_?)delPathogenic
929331GRCh37/hg19 22q11.21(chr22:18886915-21463730)x1Pathogenic

SpliceAI

347 predictions. Top by Δscore:

VariantEffectΔscore
22:19149424:G:GCacceptor_gain1.0000
22:19149658:CTCA:Cdonor_loss1.0000
22:19149659:TCAC:Tdonor_loss1.0000
22:19149660:CAC:Cdonor_loss1.0000
22:19149661:A:ACdonor_gain1.0000
22:19149661:A:Cdonor_loss1.0000
22:19149662:C:CCdonor_gain1.0000
22:19149346:C:Adonor_gain0.9900
22:19149661:ACCT:Adonor_gain0.9900
22:19149662:CCT:Cdonor_gain0.9900
22:19149662:CCTC:Cdonor_gain0.9900
22:19149415:C:CTacceptor_gain0.9800
22:19149416:A:Tacceptor_gain0.9800
22:19149424:G:Cacceptor_gain0.9800
22:19149657:ACTC:Adonor_loss0.9800
22:19149426:G:Cacceptor_gain0.9700
22:19149656:CACT:Cdonor_loss0.9700
22:19149183:T:TAdonor_gain0.9600
22:19150023:AC:Adonor_gain0.9600
22:19150024:CC:Cdonor_gain0.9600
22:19149183:TCGCA:Tdonor_gain0.9500
22:19149249:G:Adonor_gain0.9500
22:19149322:T:TAdonor_gain0.9500
22:19149426:G:GCacceptor_gain0.9500
22:19149718:A:ACdonor_gain0.9500
22:19149719:C:CCdonor_gain0.9500
22:19150018:CACT:Cdonor_loss0.9500
22:19150019:ACTC:Adonor_loss0.9500
22:19150020:CTCA:Cdonor_loss0.9500
22:19150021:T:TAdonor_loss0.9500

AlphaMissense

1285 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
22:19149083:T:CN176D0.999
22:19149087:G:CF174L0.999
22:19149087:G:TF174L0.999
22:19149089:A:GF174L0.999
22:19149727:T:CY150C0.999
22:19149741:G:CF145L0.999
22:19149741:G:TF145L0.999
22:19149743:A:GF145L0.999
22:19149777:G:CF133L0.999
22:19149777:G:TF133L0.999
22:19149778:A:CF133C0.999
22:19149778:A:GF133S0.999
22:19149779:A:GF133L0.999
22:19149081:G:CN176K0.998
22:19149081:G:TN176K0.998
22:19149082:T:CN176S0.998
22:19149082:T:GN176T0.998
22:19149084:C:AK175N0.998
22:19149084:C:GK175N0.998
22:19149088:A:GF174S0.998
22:19149728:A:GY150H0.998
22:19149742:A:CF145C0.998
22:19149742:A:GF145S0.998
22:19149082:T:AN176I0.997
22:19149743:A:TF145I0.997
22:19149754:A:TL141H0.997
22:19149069:T:AK180N0.996
22:19149069:T:GK180N0.996
22:19149080:G:TR177S0.996
22:19149088:A:CF174C0.996

dbSNP variants (sampled 300 via entrez): RS1000833361 (22:19151594 C>G), RS1000906962 (22:19151853 A>G), RS1001015822 (22:19146688 A>G), RS1001099218 (22:19152029 G>A), RS1001983311 (22:19149212 G>A,C), RS1003190868 (22:19148600 A>G), RS1004952958 (22:19149232 G>A,C), RS1005261635 (22:19149337 C>A), RS1005847943 (22:19148771 C>A,G,T), RS1007695058 (22:19151231 G>A,C), RS1008364609 (22:19148800 G>A,C,T), RS1009113176 (22:19149555 G>A,C), RS1009470297 (22:19149719 C>G,T), RS1010627674 (22:19146713 A>T), RS1011723882 (22:19149203 G>T)

Disease associations

OMIM: gene MIM:601845 | disease phenotypes: MIM:188400

GenCC curated gene-disease

Mondo (1): DiGeorge syndrome (MONDO:0008564)

Orphanet (1): 22q11.2 deletion syndrome (Orphanet:567)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST001639_30Metabolite levels3.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004723coronary artery calcification

MeSH disease descriptors (1)

DescriptorNameTree numbers
D004062DiGeorge SyndromeC05.660.207.103.500; C14.240.400.021.500; C14.280.400.044.500; C15.604.451.249.500; C16.131.077.019.500; C16.131.240.400.021.500; C16.131.260.019.500; C16.131.482.249.500; C16.131.621.207.103.500; C16.320.180.019.500; C19.642.482.500.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

ChemicalActions (top 5)PubMed papers
Resveratrolaffects cotreatment, decreases expression1
Benzo(a)pyreneaffects methylation1
Cadmiumincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Valproic Acidincreases methylation1
Asbestos, Crocidolitedecreases methylation1
Asbestos, Amositedecreases methylation1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00395538PHASE3TERMINATEDEffects of PTH Replacement on Bone in Hypoparathyroidism
NCT00576407PHASE2COMPLETEDThymus Transplantation in DiGeorge Syndrome #668
NCT00576836PHASE2COMPLETEDThymus Transplantation Dose in DiGeorge #932
NCT01821781PHASE2ACTIVE_NOT_RECRUITINGImmune Disorder HSCT Protocol
NCT05149898PHASE2COMPLETEDOpen-Label Study of ZYN002 Administered as a Transdermal Gel to Children and Adolescents With 22q11.2 Deletion Syndrome (INSPIRE)
NCT07284641PHASE2RECRUITINGHematopoietic Stem Cell Transplantation (HSCT) for Common Variable Immunodeficiency (CVID) and Other Autoimmune Manifestations of Primary Immune Regulatory Disorders (PIRD)
NCT00566488PHASE1COMPLETEDParathyroid and Thymus Transplantation in DiGeorge #931
NCT00579709PHASE1COMPLETEDThymus Transplantation With Immunosuppression
NCT00849888PHASE1TERMINATEDSerum-Free Thymus Transplantation in DiGeorge Anomaly
NCT02895906PHASE1COMPLETEDSafety and Efficacy Study of NFC-1 in Subjects Aged 12-17 Years With 22q11.2DS & Associated Neuropsychiatric Conditions
NCT00579527PHASE1/PHASE2COMPLETEDPhase I/II Thymus Transplantation With Immunosuppression #950
NCT00004351Not specifiedCOMPLETEDStudy of Phenotype and Genotype Correlations in Patients With Contiguous Gene Deletion Syndromes
NCT00005102Not specifiedUNKNOWNImmunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT00105274Not specifiedCOMPLETEDVelocardiofacial (VCFS; 22q11.2; DiGeorge) Syndrome Study
NCT00278005Not specifiedTERMINATEDInfection in DiGeorge Following CHD Surgery
NCT00556530Not specifiedRECRUITINGExamining Genetic Factors That Affect the Severity of 22q11.2 Deletion Syndrome
NCT00916955Not specifiedCOMPLETEDGenetic Modifiers for 22q11.2 Syndrome
NCT01220531Not specifiedCOMPLETEDThymus Transplantation Safety-Efficacy
NCT01781923Not specifiedCOMPLETEDCognitive Remediation in 22q11DS
NCT02381457Not specifiedCOMPLETEDSNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT02430584Not specifiedUNKNOWNWhole Blood Specimen Collection From Pregnant Subjects
NCT02460328Not specifiedCOMPLETEDResolution of Primary Immune Defect in 22q11.2 Deletion Syndrome
NCT02787486Not specifiedCOMPLETEDExpanded Noninvasive Genomic Medical Assessment: The Enigma Study
NCT03284060Not specifiedTERMINATEDSocial Cognition Training and Cognitive Remediation
NCT04141540Not specifiedCOMPLETEDMolecular Variants Associated With Schizophrenia: Differential Analysis of Monozygotic Twins With Variable Phenotypic 22q11
NCT04373226Not specifiedTERMINATEDArithmetic Abilities in Children With 22q11.2DS
NCT04639388Not specifiedRECRUITINGUnderstanding of Psychotic Disorders in Children With 22q11.2DS
NCT04639960Not specifiedTERMINATEDNeuroprotective Effects of Risperdal on Brain and Cognition in 22q11 Deletion Syndrome
NCT04647500Not specifiedCOMPLETEDEffects of Methylphenidate on Brain and Cognition in 22q11 Deletion Syndrome
NCT05924347Not specifiedRECRUITINGEarly Scoliotic Changes in Children at Increased Risk for Scoliosis Development
NCT07493096Not specifiedRECRUITINGIntensive Multimodal Neurorehabilitation Targeting Neuroplasticity in Pediatric Neurodevelopmental and Chromosomal Disorders
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): DiGeorge syndrome