RHBDF2
Basic information
Region (hg38): 17:76470891-76501790
Previous symbols: [ "RHBDL6", "TOC" ]
Links
Phenotypes
GenCC
Source:
- palmoplantar keratoderma-esophageal carcinoma syndrome (Strong), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Strong), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Supportive), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Moderate), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Definitive), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Definitive), mode of inheritance: AD
- palmoplantar keratoderma-esophageal carcinoma syndrome (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Tylosis with esophageal cancer | AD | Oncologic | Surveillance and early detection of and treatment for malignancy may decrease morbidity and mortality; Individuals may be at especially high risk of esophageal cancer with tobacco use | Dermatologic; Gastrointestinal; Oncologic | 13209063; 8508402; 8666405; 8651714; 22265016 |
ClinVar
This is a list of variants' phenotypes submitted to
- Palmoplantar_keratoderma-esophageal_carcinoma_syndrome (216 variants)
- not_provided (213 variants)
- Inborn_genetic_diseases (118 variants)
- RHBDF2-related_disorder (14 variants)
- not_specified (6 variants)
- Hepatoblastoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHBDF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001005498.4. 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 | 51 | 64 | ||||
missense | 239 | 40 | 284 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 2 | 251 | 91 | 8 |
Highest pathogenic variant AF is 0.0000020665
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RHBDF2 | protein_coding | protein_coding | ENST00000313080 | 17 | 30900 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00119 | 0.999 | 125714 | 0 | 32 | 125746 | 0.000127 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.79 | 432 | 550 | 0.785 | 0.0000371 | 5505 |
Missense in Polyphen | 148 | 228.83 | 0.64676 | 2302 | ||
Synonymous | 0.742 | 215 | 229 | 0.938 | 0.0000157 | 1674 |
Loss of Function | 4.04 | 13 | 40.9 | 0.318 | 0.00000200 | 430 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000483 | 0.000474 |
Ashkenazi Jewish | 0.000103 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000143 | 0.000139 |
European (Non-Finnish) | 0.0000720 | 0.0000703 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000164 | 0.000163 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Rhomboid protease-like protein which has no protease activity but regulates the secretion of several ligands of the epidermal growth factor receptor. Indirectly activates the epidermal growth factor receptor signaling pathway and may thereby regulate sleep, cell survival, proliferation and migration (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.756
- rvis_EVS
- -0.37
- rvis_percentile_EVS
- 28.29
Haploinsufficiency Scores
- pHI
- 0.228
- hipred
- Y
- hipred_score
- 0.639
- ghis
- 0.549
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.650
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rhbdf2
- Phenotype
- liver/biliary system 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); hematopoietic system 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); pigmentation 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); vision/eye phenotype; immune system phenotype; cellular phenotype; skeleton 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); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- proteolysis;protein transport;regulation of epidermal growth factor receptor signaling pathway;regulation of protein secretion;negative regulation of protein secretion
- Cellular component
- endoplasmic reticulum membrane;plasma membrane;integral component of membrane
- Molecular function
- serine-type endopeptidase activity;growth factor binding