RFNG
Basic information
Region (hg38): 17:82047902-82051831
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (60 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFNG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002917.2. 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 | 3 | |||||
| missense | 54 | 60 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 54 | 8 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RFNG | protein_coding | protein_coding | ENST00000310496 | 8 | 3930 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.79e-9 | 0.0549 | 125466 | 0 | 27 | 125493 | 0.000108 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.234 | 152 | 160 | 0.948 | 0.00000994 | 2090 |
| Missense in Polyphen | 80 | 91.239 | 0.87682 | 1006 | ||
| Synonymous | -3.49 | 103 | 66.8 | 1.54 | 0.00000440 | 694 |
| Loss of Function | -0.468 | 12 | 10.4 | 1.16 | 4.42e-7 | 136 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000121 | 0.000120 |
| Ashkenazi Jewish | 0.0000997 | 0.0000995 |
| East Asian | 0.000218 | 0.000218 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000920 | 0.0000882 |
| Middle Eastern | 0.000218 | 0.000218 |
| South Asian | 0.000308 | 0.000294 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Glycosyltransferase that initiates the elongation of O- linked fucose residues attached to EGF-like repeats in the extracellular domain of Notch molecules. Modulates NOTCH1 activity by modifying O-fucose residues at specific EGF-like domains resulting in enhancement of NOTCH1 activation by DLL1 and JAG1. May be involved in limb formation and in neurogenesis. {ECO:0000250|UniProtKB:O09009, ECO:0000250|UniProtKB:O12972, ECO:0000250|UniProtKB:Q9R1U9}.;
- Pathway
- Other types of O-glycan biosynthesis - Homo sapiens (human);Notch signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Notch Signaling Pathway;Notch Signaling Pathway;Signal Transduction;Notch;Pre-NOTCH Processing in Golgi;Pre-NOTCH Expression and Processing;Signaling by NOTCH
(Consensus)
Recessive Scores
- pRec
- 0.120
Haploinsufficiency Scores
- pHI
- 0.169
- hipred
- N
- hipred_score
- 0.301
- ghis
- 0.480
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.448
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rfng
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; skeleton phenotype; embryo 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); normal phenotype; digestive/alimentary phenotype; limbs/digits/tail phenotype;
Zebrafish Information Network
- Gene name
- rfng
- Affected structure
- fourth ventricle
- Phenotype tag
- abnormal
- Phenotype quality
- structure
Gene ontology
- Biological process
- pattern specification process;nervous system development;regulation of Notch signaling pathway;animal organ morphogenesis;cell differentiation;positive regulation of protein binding;protein O-linked fucosylation;positive regulation of Notch signaling pathway
- Cellular component
- extracellular region;integral component of Golgi membrane
- Molecular function
- molecular_function;acetylglucosaminyltransferase activity;O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity;metal ion binding