GDF1

gene
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Summary

GDF1 (growth differentiation factor 1, HGNC:4214) is a protein-coding gene on chromosome 19p13.11, encoding Embryonic growth/differentiation factor 1 (P27539). May mediate cell differentiation events during embryonic development.

This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. Studies in rodents suggest that this protein is involved in the establishment of left-right asymmetry in early embryogenesis and in neural development in later embryogenesis. The encoded protein is translated from a bicistronic mRNA that also encodes ceramide synthase 1. Mutations in this gene are associated with several congenital cardiovascular malformations.

Source: NCBI Gene 2657 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): right atrial isomerism (Strong, GenCC) — +2 more curated relationships
  • Clinical variants (ClinVar): 48 total — 2 pathogenic
  • Phenotypes (HPO): 39
  • MANE Select transcript: NM_001492

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:4214
Approved symbolGDF1
Namegrowth differentiation factor 1
Location19p13.11
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000130283
Ensembl biotypeprotein_coding
OMIM602880
Entrez2657

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000247005

RefSeq mRNA: 2 — MANE Select: NM_001492 NM_001387438, NM_001492

CCDS: CCDS42526

Canonical transcript exons

ENST00000247005 — 8 exons

ExonStartEnd
ENSE000032168081889582418896158
ENSE000034871921887893018879039
ENSE000035147871886854518869390
ENSE000035962441886998318870619
ENSE000036052221889341618893575
ENSE000036236671888027418880435
ENSE000036343511888408718884267
ENSE000036629861887924118879388

Expression profiles

Bgee: expression breadth broad, 34 present calls, max score 64.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.0664 / max 340.4213, expressed in 983 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
18010411.0664983
1801051.2490464

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primary visual cortexUBERON:000243664.32gold quality
sural nerveUBERON:001548862.40silver quality
superior frontal gyrusUBERON:000266161.19gold quality
ganglionic eminenceUBERON:000402351.90gold quality
skeletal muscle tissueUBERON:000113444.86gold quality
cortical plateUBERON:000534343.03gold quality
colonic epitheliumUBERON:000039741.50gold quality
muscle tissueUBERON:000238539.50gold quality
prefrontal cortexUBERON:000045138.98gold quality
hindlimb stylopod muscleUBERON:000425238.44gold quality
ventricular zoneUBERON:000305336.48gold quality
bone marrow cellCL:000209236.16gold quality
frontal cortexUBERON:000187032.29gold quality
bone marrowUBERON:000237131.74gold quality
tonsilUBERON:000237231.69gold quality
stromal cell of endometriumCL:000225529.87gold quality
liverUBERON:000210729.66gold quality
duodenumUBERON:000211428.14gold quality
olfactory segment of nasal mucosaUBERON:000538628.04gold quality
lymph nodeUBERON:000002927.57gold quality
cerebral cortexUBERON:000095627.23gold quality
Brodmann (1909) area 9UBERON:001354026.62gold quality
islet of LangerhansUBERON:000000626.55gold quality
vermiform appendixUBERON:000115426.42gold quality
gall bladderUBERON:000211025.98gold quality
pancreasUBERON:000126425.86gold quality
placentaUBERON:000198725.83gold quality
muscle of legUBERON:000138325.82gold quality
bloodUBERON:000017825.73gold quality
urinary bladderUBERON:000125525.72gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 13)

  • Heterozygous loss-of-function mutations in the human GDF1 gene contribute to cardiac defects ranging from tetralogy of Fallot to transposition of the great arteries. (PMID:17924340)
  • GDF1 expression is correlated with progression and aggressive behaviors in cervical cancer, suggesting a tumor-promoting role for GDF1 in the progression of this malignancy. (PMID:19359031)
  • Molecular genetic basis of a kindred with 5 siblings with right atrial isomerism involved mutations in GDF1. (PMID:20413652)
  • GDF1 may be associated with congenital heart defects risk, and these variations contribute at least in part to the development of some subtypes of conotruncal defects in the Chinese Han population. (PMID:23076529)
  • indicate that the expression of growth/differentiation factor 1 (GDF1) is up-regulated in human dilated cardiomyopathy (DCM)hearts and murine hypertrophic hearts. (PMID:24275554)
  • This implies that Gdf1 potentiates Nodal activity by stabilizing a low molecular weight fraction that is susceptible to neutralization by soluble Acvr2. (PMID:24798330)
  • Our results suggest that the GDF1 rs4808863 polymorphism contributes to an increased risk of fetal CHDs, especially the subtypes of AVSD, LVOTO and left-right laterality defects. (PMID:26656983)
  • Rare inherited and de novo variants in 2,871 congenital heart disease probands identified GDF1, MYH6, and FLT4 as causative genes. (PMID:28991257)
  • Nkx2.5 acts upstream of GDF1 and the genetic variants in GDF1 promoter may confer genetic susceptibility to sporadic CHD potentially by altering its expression. (PMID:31171573)
  • A founder truncating variant in GDF1 causes autosomal-recessive right isomerism and associated congenital heart defects in multiplex Arab kindreds. (PMID:32144877)
  • Arsenic suppresses GDF1 expression via ROS-dependent downregulation of specificity protein 1. (PMID:33360347)
  • Homozygous variants in the GDF1 gene related to recurrent right isomerism and complex CHD in two Indian families. (PMID:35351224)
  • Human colorectal cancer: upregulation of the adaptor protein Rai in TILs leads to cell dysfunction by sustaining GSK-3 activation and PD-1 expression. (PMID:38175205)

Cross-species orthologs

1 orthologs

OrganismSymbolGene ID
mus_musculusGdf1ENSMUSG00000109523

Paralogs (31): TGFB2 (ENSG00000092969), BMP7 (ENSG00000101144), TGFB1 (ENSG00000105329), BMP5 (ENSG00000112175), BMP8B (ENSG00000116985), TGFB3 (ENSG00000119699), INHBA (ENSG00000122641), INHA (ENSG00000123999), BMP4 (ENSG00000125378), BMP2 (ENSG00000125845), GDF5 (ENSG00000125965), BMP15 (ENSG00000130385), GDF15 (ENSG00000130513), GDF11 (ENSG00000135414), MSTN (ENSG00000138379), INHBE (ENSG00000139269), LEFTY2 (ENSG00000143768), GDF7 (ENSG00000143869), BMP3 (ENSG00000152785), BMP6 (ENSG00000153162), GDF6 (ENSG00000156466), NODAL (ENSG00000156574), INHBB (ENSG00000163083), BMP10 (ENSG00000163217), GDF9 (ENSG00000164404), INHBC (ENSG00000175189), BMP8A (ENSG00000183682), GDF3 (ENSG00000184344), LEFTY1 (ENSG00000243709), GDF2 (ENSG00000263761), GDF10 (ENSG00000266524)

Protein

Protein identifiers

Embryonic growth/differentiation factor 1P27539 (reviewed: P27539)

All UniProt accessions (1): P27539

UniProt curated annotations — full annotation on UniProt →

Function. May mediate cell differentiation events during embryonic development.

Subunit / interactions. Homodimer; disulfide-linked.

Subcellular location. Secreted.

Tissue specificity. Expressed in the brain.

Disease relevance. Conotruncal heart malformations (CTHM) [MIM:217095] A group of congenital heart defects involving the outflow tracts. Examples include truncus arteriosus communis, double-outlet right ventricle and transposition of great arteries. Truncus arteriosus communis is characterized by a single outflow tract instead of a separate aorta and pulmonary artery. In transposition of the great arteries, the aorta arises from the right ventricle and the pulmonary artery from the left ventricle. In double outlet of the right ventricle, both the pulmonary artery and aorta arise from the right ventricle. The disease is caused by variants affecting the gene represented in this entry. Congenital heart defects, multiple types, 6 (CHTD6) [MIM:613854] An autosomal dominant disorder characterized by congenital developmental abnormalities involving structures of the heart. Common defects include tetralogy of Fallot, transposition of the great arteries, double-outlet right ventricle, total anomalous pulmonary venous return, pulmonary stenosis or atresia, atrioventricular canal, ventricular septal defect, and hypoplastic left or right ventricle. The disease is caused by variants affecting the gene represented in this entry. Tetralogy of Fallot (TOF) [MIM:187500] A congenital heart anomaly which consists of pulmonary stenosis, ventricular septal defect, dextroposition of the aorta (aorta is on the right side instead of the left) and hypertrophy of the right ventricle. In this condition, blood from both ventricles (oxygen-rich and oxygen-poor) is pumped into the body often causing cyanosis. The disease is caused by variants affecting the gene represented in this entry. Right atrial isomerism (RAI) [MIM:208530] A severe complex congenital heart defect resulting from embryonic disruption of proper left-right axis determination. RAI is usually characterized by complete atrioventricular septal defect with a common atrium and univentricular AV connection, total anomalous pulmonary drainage, and transposition or malposition of the great arteries. Affected individuals present at birth with severe cardiac failure. Other associated abnormalities include bilateral trilobed lungs, midline liver, and asplenia, as well as situs inversus affecting other organs. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. This protein is produced by a bicistronic gene which also produces the CERS1 protein from a non-overlapping reading frame.

Similarity. Belongs to the TGF-beta family.

RefSeq proteins (2): NP_001374367, NP_001483* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001839TGF-b_CDomain
IPR015615TGF-beta-likeFamily
IPR017948TGFb_CSConserved_site
IPR029034Cystine-knot_cytokineHomologous_superfamily

Pfam: PF00019

UniProt features (20 total): sequence variant 11, disulfide bond 4, signal peptide 1, propeptide 1, chain 1, region of interest 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P27539-F174.440.21

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (4): 267–337, 296–369, 300–371, 336

Glycosylation sites (1): 206

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-1181150Signaling by NODAL

MSigDB gene sets: 133 (showing top): GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOMF_GROWTH_FACTOR_ACTIVITY, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_ENDODERM_DEVELOPMENT, GOBP_RESPONSE_TO_BMP, GOBP_RESPONSE_TO_GROWTH_FACTOR, GOMF_CYTOKINE_ACTIVITY, VDR_Q3, LEF1_Q6, GOBP_EMBRYO_DEVELOPMENT, GOBP_MESODERM_DEVELOPMENT, GOMF_SIGNALING_RECEPTOR_BINDING, RAAGNYNNCTTY_UNKNOWN

GO Biological Process (6): in utero embryonic development (GO:0001701), endoderm development (GO:0007492), mesoderm development (GO:0007498), BMP signaling pathway (GO:0030509), regulation of transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0090092), signal transduction (GO:0007165)

GO Molecular Function (2): cytokine activity (GO:0005125), growth factor activity (GO:0008083)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Developmental Biology1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
tissue development2
receptor ligand activity2
chordate embryonic development1
cellular response to BMP stimulus1
transforming growth factor beta receptor superfamily signaling pathway1
cell surface receptor protein serine/threonine kinase signaling pathway1
regulation of signal transduction1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cellular anatomical structure1

Protein interactions and networks

STRING

1062 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GDF1CERS2Q96G23934
GDF1ACVR1CQ8NER5883
GDF1CERS4Q9HA82883
GDF1CERS6Q6ZMG9876
GDF1CRIPTOP13385868
GDF1CFC1P0CG37861
GDF1CERS5Q8N5B7796
GDF1CERS3Q8IU89785
GDF1ACVR2AP27037781
GDF1MED13LQ71F56739
GDF1SPTLC2O15270720
GDF1SPTLC1O15269720
GDF1SPTLC3Q9NUV7720
GDF1ACVR2BQ13705716
GDF1NKX2-6A6NCS4693

IntAct

2 interactions, top by confidence:

ABTypeScore
GDF1HTR4psi-mi:“MI:0915”(physical association)0.370

BioGRID (2): GDF1 (Two-hybrid), GDF1 (Affinity Capture-MS)

ESM2 similar proteins: A0A061IR73, A6H687, A6NKF1, D3KCC4, E1BD59, G3MY25, G3MZC5, O00634, O75064, P0C5W1, P20863, P27539, P52824, P54777, Q002B5, Q08DM2, Q0VCE3, Q13608, Q17RN3, Q2TBW5, Q3U0S6, Q4VYA0, Q53EQ6, Q561R2, Q568Y2, Q5BK61, Q5JR98, Q5RE82, Q5U651, Q6F5E8, Q6NY19, Q6ZS72, Q8BH83, Q8C052, Q8CDY7, Q8VIM9, Q8WZA9, Q90343, Q90ZN1, Q92985

Diamond homologs: A1C2U3, A1C2U6, A1C2U7, A1C2V0, A1C2V5, A8E7N9, G5EEL5, O08689, O14793, O18828, O18830, O18831, O18836, O35312, O42220, O42221, O42222, O46576, O61643, O95390, O95393, P09534, P12644, P12645, P17491, P18075, P20722, P20863, P22003, P22004, P22444, P23359, P27091, P27539, P35621, P43026, P43027, P43028, P43029, P48970

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance22
Likely benign20
Benign4

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1453078NM_001492.6(GDF1):c.626G>A (p.Trp209Ter)Pathogenic
183023NM_021267.5(CERS1):c.549C>G (p.His183Gln)Pathogenic

SpliceAI

1535 predictions. Top by Δscore:

VariantEffectΔscore
19:18878928:A:ACdonor_gain1.0000
19:18878929:C:CCdonor_gain1.0000
19:18878929:CT:Cdonor_gain1.0000
19:18878929:CTCGG:Cdonor_gain1.0000
19:18879035:ATGTA:Aacceptor_gain1.0000
19:18879036:TGTA:Tacceptor_gain1.0000
19:18879038:TA:Tacceptor_gain1.0000
19:18879039:AC:Aacceptor_loss1.0000
19:18879039:ACT:Aacceptor_loss1.0000
19:18879040:C:CCacceptor_gain1.0000
19:18879040:CTG:Cacceptor_loss1.0000
19:18879237:TCA:Tdonor_loss1.0000
19:18879237:TCACC:Tdonor_loss1.0000
19:18879238:CACCA:Cdonor_loss1.0000
19:18879239:A:ACdonor_gain1.0000
19:18879239:ACCAG:Adonor_loss1.0000
19:18879240:C:CCdonor_gain1.0000
19:18879240:C:Gdonor_loss1.0000
19:18879387:ACCTG:Aacceptor_loss1.0000
19:18880266:CCA:Cdonor_gain1.0000
19:18880269:CTCA:Cdonor_loss1.0000
19:18880270:TCAC:Tdonor_loss1.0000
19:18880271:CA:Cdonor_loss1.0000
19:18880272:A:ACdonor_gain1.0000
19:18880272:AC:Adonor_gain1.0000
19:18880273:C:CAdonor_gain1.0000
19:18880273:CC:Cdonor_gain1.0000
19:18880273:CCAG:Cdonor_gain1.0000
19:18880398:CG:Cacceptor_gain1.0000
19:18880433:TAC:Tacceptor_gain1.0000

AlphaMissense

2303 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:18868844:A:CF291C0.999
19:18868873:C:AW281C0.998
19:18868873:C:GW281C0.998
19:18868889:A:CF276C0.998
19:18868843:G:CF291L0.997
19:18868843:G:TF291L0.997
19:18868844:A:GF291S0.997
19:18868845:A:GF291L0.997
19:18868864:C:AW284C0.997
19:18868864:C:GW284C0.997
19:18868888:G:CF276L0.996
19:18868888:G:TF276L0.996
19:18868890:A:GF276L0.996
19:18868889:A:GF276S0.993
19:18868673:A:TL348H0.991
19:18868643:A:GL358P0.990
19:18868859:A:TI286N0.990
19:18868890:A:TF276I0.990
19:18868829:C:TC296Y0.989
19:18868829:C:GC296S0.988
19:18868830:A:TC296S0.988
19:18868835:T:AN294I0.988
19:18868624:C:AM364I0.987
19:18868624:C:GM364I0.987
19:18868624:C:TM364I0.987
19:18868706:C:TC337Y0.987
19:18868664:T:AD351V0.986
19:18868669:G:CF349L0.986
19:18868669:G:TF349L0.986
19:18868671:A:GF349L0.986

dbSNP variants (sampled 300 via entrez): RS1000062904 (19:18868605 A>AG), RS1000168129 (19:18880936 C>T), RS1000275000 (19:18885438 C>T), RS1000287033 (19:18897391 C>CCCGCCA), RS1000292527 (19:18877606 G>C,T), RS1000450783 (19:18897161 AC>A,ACC), RS1000542322 (19:18873265 T>C), RS1000573480 (19:18873010 C>G,T), RS1000606848 (19:18891486 C>G,T), RS1000660977 (19:18892680 C>G), RS1000663212 (19:18885795 G>A), RS1000744427 (19:18886617 C>T), RS1000770254 (19:18879177 G>A,T), RS1000815859 (19:18875900 G>A,C), RS1000843398 (19:18876186 A>G)

Disease associations

OMIM: gene MIM:602880 | disease phenotypes: MIM:616230, MIM:306955, MIM:613854

GenCC curated gene-disease

DiseaseClassificationInheritance
right atrial isomerismStrongAutosomal recessive
congenital heart defects, multiple types, 6StrongAutosomal dominant
conotruncal heart malformationsLimitedUnknown

Mondo (5): progressive myoclonic epilepsy type 8 (MONDO:0014545), visceral heterotaxy (MONDO:0018677), congenital heart defects, multiple types, 6 (MONDO:0013463), right atrial isomerism (MONDO:0008832), conotruncal heart malformations (MONDO:0016581)

Orphanet (4): Progressive myoclonic epilepsy type 8 (Orphanet:424027), Visceral heterotaxy (Orphanet:450), Congenitally uncorrected transposition of the great arteries (Orphanet:860), Situs ambiguus (Orphanet:157769)

HPO phenotypes

39 total (30 of 39 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000233Thin vermilion border
HP:0000268Dolichocephaly
HP:0000337Broad forehead
HP:0000520Proptosis
HP:0001156Brachydactyly
HP:0001274Agenesis of corpus callosum
HP:0001511Intrauterine growth retardation
HP:0001629Ventricular septal defect
HP:0001631Atrial septal defect
HP:0001636Tetralogy of Fallot
HP:0001642Pulmonic stenosis
HP:0001651Dextrocardia
HP:0001669Transposition of the great arteries
HP:0001674Complete atrioventricular canal defect
HP:0001680Coarctation of aorta
HP:0001684Secundum atrial septal defect
HP:0001696Situs inversus totalis
HP:0001719Double outlet right ventricle
HP:0001746Asplenia
HP:0001748Polysplenia
HP:0001750Single ventricle
HP:0002101Abnormal lung lobation
HP:0004209Clinodactyly of the 5th finger
HP:0004467Preauricular pit
HP:0004935Pulmonary artery atresia
HP:0005105Abnormal nasal morphology

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, decreases reaction, affects reaction, affects binding2
Benzo(a)pyrenedecreases methylation, increases expression2
Folic Aciddecreases expression, decreases reaction2
Tobacco Smoke Pollutiondecreases expression, increases expression2
piceneincreases expression1
Resveratroldecreases expression1
Sunitinibincreases expression1
Acetylcysteinedecreases expression, decreases reaction1
Cisplatindecreases expression1
Doxorubicindecreases expression1
Dustdecreases expression1
Fluorouracilaffects reaction, decreases expression1
Hydrogen Peroxidedecreases expression, decreases reaction1
Leadaffects expression1
Mustard Gasaffects expression, affects reaction1
Nicotineincreases expression1
Dronabinolincreases expression1
Valproic Acidincreases methylation1
2-Naphthylamineincreases expression1
Permethrinincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04009863Not specifiedCOMPLETEDHIFU Ablation vs Fixed-dose RAI-131 Therapy in Moderate-sized Non-toxic MNG
NCT00004361Not specifiedCOMPLETEDStudy of the Relationship Between Calcium Levels and Intact Parathyroid Hormone (iPTH) in Adults With Repaired or Palliated Conotruncal Cardiac Defects
NCT00005102Not specifiedUNKNOWNImmunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT01460316Not specifiedCOMPLETEDConotruncal Cardiac Defects and Nutrigenetic Etiopathogeny
NCT01591928Not specifiedCOMPLETEDHeterotaxy Syndrome and Intestinal Rotation Abnormalities - A Prospective Study
NCT01929967Not specifiedCOMPLETEDDefining Immunodeficiency in Heterotaxy Syndrome: Pilot Study Data
NCT02432079Not specifiedRECRUITINGMolecular Genetics of Heterotaxy and Related Congenital Heart Defects