RASGRP4

RAS guanyl releasing protein 4, the group of EF-hand domain containing

Basic information

Region (hg38): 19:38409051-38426305

Links

ENSG00000171777 ∙ NCBI:115727 ∙ OMIM:607320 ∙ HGNC:18958 ∙ Uniprot:Q8TDF6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RASGRP4 gene.

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.

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					1	1
missense			35	1	1	37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	2

Variants in RASGRP4

This is a list of pathogenic ClinVar variants found in the RASGRP4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-38410048-C-G		not specified	Uncertain significance (May 05, 2022)
19-38410939-G-A		not specified	Uncertain significance (Jul 14, 2021)
19-38410968-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-38410969-A-G		not specified	Uncertain significance (Apr 12, 2022)
19-38411157-C-T		not specified	Uncertain significance (Jul 12, 2022)
19-38411172-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-38411201-T-C		not specified	Uncertain significance (Dec 20, 2023)
19-38411224-G-T		not specified	Uncertain significance (Feb 14, 2024)
19-38411368-G-A		not specified	Uncertain significance (Nov 03, 2022)
19-38412690-G-A			Benign (Sep 15, 2018)
19-38412938-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-38412976-T-C		not specified	Uncertain significance (Oct 05, 2021)
19-38413018-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-38413414-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-38414853-G-A		not specified	Uncertain significance (Feb 21, 2024)
19-38414877-C-T		not specified	Uncertain significance (May 09, 2023)
19-38414924-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-38414979-C-T		not specified	Uncertain significance (Apr 13, 2023)
19-38415065-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-38415066-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-38415069-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-38415075-G-A		not specified	Likely benign (Dec 14, 2021)
19-38415075-G-C			Benign (Aug 08, 2018)
19-38415078-C-T		not specified	Uncertain significance (May 03, 2023)
19-38417100-G-C		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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