GDF11
growth differentiation factor 11, the group of Transforming growth factor beta superfamily
Basic information
Region (hg38): 12:55743122-55757264
Links
Phenotypes
GenCC
Source:
- vertebral hypersegmentation and orofacial anomalies (Strong), mode of inheritance: AD
- vertebral hypersegmentation and orofacial anomalies (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Vertebral hypersegmentation and orofacial anomalies | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal | 31215115 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (26 variants)
- not_provided (9 variants)
- Vertebral_hypersegmentation_and_orofacial_anomalies (6 variants)
- GDF11-related_disorder (3 variants)
- Orofacial_cleft (1 variants)
- GDF11-associated_multiple_congenital_anomalies_and_ID (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDF11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005811.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 31 | 33 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 36 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GDF11 | protein_coding | protein_coding | ENST00000257868 | 3 | 13848 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.976 | 0.0235 | 125736 | 0 | 2 | 125738 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.98 | 104 | 232 | 0.449 | 0.0000140 | 2613 |
| Missense in Polyphen | 18 | 69.311 | 0.2597 | 689 | ||
| Synonymous | 1.67 | 71 | 91.3 | 0.778 | 0.00000524 | 853 |
| Loss of Function | 3.47 | 1 | 15.9 | 0.0628 | 9.22e-7 | 151 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Secreted signal that acts globally to specify positional identity along the anterior/posterior axis during development. May play critical roles in patterning both mesodermal and neural tissues and in establishing the skeletal pattern (By similarity). Signals through activin receptors type-2, ACVR2A and ACVR2B, and activin receptors type-1, ACVR1B, ACVR1C and TGFBR1 leading to the phosphorylation of SMAD2 and SMAD3 (PubMed:28257634). {ECO:0000250|UniProtKB:Q9Z1W4, ECO:0000269|PubMed:28257634}.;
- Pathway
- TGF-Core;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;TGF-beta super family signaling pathway canonical;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;GPCR signaling-G alpha i;BMP2 signaling TGF-beta MV;BMP signaling Dro
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.230
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.599
- hipred
- Y
- hipred_score
- 0.729
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.611
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gdf11
- Phenotype
- immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; embryo phenotype; respiratory system phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; taste/olfaction phenotype;
Zebrafish Information Network
- Gene name
- gdf11
- Affected structure
- exocrine pancreas
- Phenotype tag
- abnormal
- Phenotype quality
- increased size
Gene ontology
- Biological process
- skeletal system development;metanephros development;ureteric bud development;nervous system development;mesoderm development;negative regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of pathway-restricted SMAD protein phosphorylation;spinal cord anterior/posterior patterning;pancreas development;regulation of apoptotic process;regulation of MAPK cascade;negative regulation of neuron differentiation;cell development;cell maturation;camera-type eye morphogenesis;roof of mouth development;SMAD protein signal transduction
- Cellular component
- cellular_component;extracellular space;nucleoplasm;protein-containing complex;intracellular membrane-bounded organelle
- Molecular function
- cytokine activity;transforming growth factor beta receptor binding;protein binding;growth factor activity