RASGRP4
Basic information
Region (hg38): 19:38409051-38426305
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (86 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASGRP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000170604.3. 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 | 1 | |||||
missense | 81 | 87 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 81 | 5 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RASGRP4 | protein_coding | protein_coding | ENST00000587738 | 17 | 17251 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0376 | 0.962 | 124636 | 0 | 28 | 124664 | 0.000112 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.05 | 291 | 408 | 0.714 | 0.0000250 | 4299 |
Missense in Polyphen | 92 | 160.45 | 0.57341 | 1793 | ||
Synonymous | 1.29 | 142 | 163 | 0.871 | 0.00000974 | 1356 |
Loss of Function | 4.11 | 10 | 37.0 | 0.270 | 0.00000214 | 378 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000278 | 0.000277 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000167 | 0.000167 |
Finnish | 0.0000489 | 0.0000464 |
European (Non-Finnish) | 0.000137 | 0.000133 |
Middle Eastern | 0.000167 | 0.000167 |
South Asian | 0.0000357 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functions as a cation- and diacylglycerol (DAG)- regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP. May function in mast cells differentiation. {ECO:0000269|PubMed:11880369, ECO:0000269|PubMed:11956218, ECO:0000269|PubMed:12493770, ECO:0000269|PubMed:18024961}.;
- Pathway
- Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);MAPK Signaling Pathway;Ras Signaling;Regulation of Ras family activation;Signal Transduction;Fc epsilon receptor (FCERI) signaling;Innate Immune System;Immune System;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;FCERI mediated NF-kB activation
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.668
- rvis_EVS
- -0.04
- rvis_percentile_EVS
- 50.5
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- Y
- hipred_score
- 0.655
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.481
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rasgrp4
- Phenotype
- hematopoietic system phenotype; pigmentation phenotype; digestive/alimentary phenotype; vision/eye phenotype; immune system phenotype; skeleton phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- rasgrp4
- Affected structure
- thoracic duct
- Phenotype tag
- abnormal
- Phenotype quality
- hypoplastic
Gene ontology
- Biological process
- MAPK cascade;transmembrane receptor protein tyrosine kinase signaling pathway;activation of phospholipase C activity;small GTPase mediated signal transduction;regulation of G protein-coupled receptor signaling pathway;cell population proliferation;response to extracellular stimulus;myeloid cell differentiation;positive regulation of Ras protein signal transduction
- Cellular component
- cytosol;plasma membrane;membrane
- Molecular function
- Ras guanyl-nucleotide exchange factor activity;calcium ion binding;diacylglycerol binding;GTP-dependent protein binding