HBEGF
heparin binding EGF like growth factor
Basic information
Region (hg38): 5:140332843-140346603
Previous symbols: [ "HEGFL", "DTS", "DTR" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HBEGF gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 1 | 0 |
Variants in HBEGF
This is a list of pathogenic ClinVar variants found in the HBEGF region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-140334711-C-T | not specified | Uncertain significance (Apr 07, 2022) | ||
| 5-140335891-C-T | not specified | Uncertain significance (Sep 25, 2023) | ||
| 5-140342705-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 5-140342708-G-A | not specified | Uncertain significance (Dec 14, 2022) | ||
| 5-140345920-G-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 5-140345949-A-G | not specified | Uncertain significance (Sep 13, 2023) | ||
| 5-140345956-G-A | not specified | Uncertain significance (Apr 01, 2024) | ||
| 5-140346012-G-A | not specified | Likely benign (Jan 18, 2023) | ||
| 5-140346281-A-G | Uncertain significance (Apr 04, 2024) | |||
| 5-140346292-G-T | not specified | Uncertain significance (Apr 29, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HBEGF | protein_coding | protein_coding | ENST00000230990 | 5 | 13789 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0756 | 0.878 | 125743 | 0 | 4 | 125747 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 77 | 119 | 0.648 | 0.00000625 | 1310 |
| Missense in Polyphen | 28 | 51.936 | 0.53912 | 593 | ||
| Synonymous | -0.153 | 52 | 50.6 | 1.03 | 0.00000249 | 448 |
| Loss of Function | 1.69 | 3 | 8.22 | 0.365 | 3.43e-7 | 121 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Growth factor that mediates its effects via EGFR, ERBB2 and ERBB4. Required for normal cardiac valve formation and normal heart function. Promotes smooth muscle cell proliferation. May be involved in macrophage-mediated cellular proliferation. It is mitogenic for fibroblasts, but not endothelial cells. It is able to bind EGF receptor/EGFR with higher affinity than EGF itself and is a far more potent mitogen for smooth muscle cells than EGF. Also acts as a diphtheria toxin receptor.;
- Pathway
- Bladder cancer - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Epithelial cell signaling in Helicobacter pylori infection - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;EGF-Core;IL1 and megakaryocytes in obesity;Nuclear Receptors Meta-Pathway;NRF2 pathway;Photodynamic therapy-induced AP-1 survival signaling.;VEGFA-VEGFR2 Signaling Pathway;Hypertrophy Model;ErbB Signaling Pathway;SHC1 events in ERBB2 signaling;Signaling by PTK6;Signaling by GPCR;Disease;Signal Transduction;nfat and hypertrophy of the heart ;ERBB2 Activates PTK6 Signaling;Uptake and function of diphtheria toxin;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Uptake and actions of bacterial toxins;Infectious disease;PTK6 promotes HIF1A stabilization;ErbB4 signaling events;GPCR signaling-G alpha s Epac and ERK;Downregulation of ERBB2 signaling;GPCR signaling-G alpha s PKA and ERK;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;GRB2 events in ERBB2 signaling;EGFR Transactivation by Gastrin;Signaling by Non-Receptor Tyrosine Kinases;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Constitutive Signaling by Aberrant PI3K in Cancer;PI3K events in ERBB2 signaling;Signaling by ERBB2;ERBB2 Regulates Cell Motility;SHC1 events in ERBB4 signaling;PI3K/AKT Signaling in Cancer;PI3K events in ERBB4 signaling;GPCR signaling-G alpha i;Nuclear signaling by ERBB4;Signaling by ERBB4;Signaling by Receptor Tyrosine Kinases;Gastrin-CREB signalling pathway via PKC and MAPK;G alpha (q) signalling events;GPCR downstream signalling;Intracellular signaling by second messengers;LPA receptor mediated events;Diseases of signal transduction;Plasma membrane estrogen receptor signaling;ErbB receptor signaling network
(Consensus)
Recessive Scores
- pRec
- 0.432
Intolerance Scores
- loftool
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.19
Haploinsufficiency Scores
- pHI
- 0.551
- hipred
- Y
- hipred_score
- 0.704
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.945
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hbegf
- Phenotype
- skeleton 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); 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); normal phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; homeostasis/metabolism phenotype; muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- hbegfb
- Affected structure
- pericardium
- Phenotype tag
- abnormal
- Phenotype quality
- edematous
Gene ontology
- Biological process
- MAPK cascade;signal transduction;epidermal growth factor receptor signaling pathway;muscle organ development;regulation of heart contraction;positive regulation of cell population proliferation;regulation of signaling receptor activity;peptidyl-tyrosine phosphorylation;positive regulation of cell growth;positive regulation of cell migration;wound healing, spreading of epidermal cells;ERBB2 signaling pathway;phosphatidylinositol phosphorylation;positive regulation of smooth muscle cell proliferation;positive regulation of peptidyl-tyrosine phosphorylation;negative regulation of elastin biosynthetic process;positive regulation of keratinocyte migration;positive regulation of protein kinase B signaling;cell chemotaxis;positive regulation of wound healing;regulation of cell motility
- Cellular component
- extracellular region;extracellular space;plasma membrane;integral component of plasma membrane;cell surface;endocytic vesicle membrane;clathrin-coated endocytic vesicle membrane
- Molecular function
- protein tyrosine kinase activity;Ras guanyl-nucleotide exchange factor activity;epidermal growth factor receptor binding;growth factor activity;heparin binding;phosphatidylinositol-4,5-bisphosphate 3-kinase activity