RASGRP3

RAS guanyl releasing protein 3, the group of EF-hand domain containing

Basic information

Region (hg38): 2:33436323-33564750

Links

ENSG00000152689 ∙ NCBI:25780 ∙ OMIM:609531 ∙ HGNC:14545 ∙ Uniprot:Q8IV61 ∙ 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 RASGRP3 gene.

• Inborn genetic diseases (22 variants)
• not provided (4 variants)
• Lip and oral cavity carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASGRP3 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				3	1	4
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	4	1

Variants in RASGRP3

This is a list of pathogenic ClinVar variants found in the RASGRP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-33457670-G-T		Lip and oral cavity carcinoma	association (Nov 02, 2015)
2-33516640-T-G		not specified	Uncertain significance (Dec 27, 2023)
2-33519952-G-A		not specified	Uncertain significance (Feb 27, 2023)
2-33519957-G-A		not specified	Likely benign (Aug 12, 2021)
2-33520009-C-T			Likely benign (Jun 26, 2018)
2-33520665-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-33521973-G-A		not specified	Uncertain significance (Jul 16, 2021)
2-33522003-C-T			Benign (Jul 10, 2017)
2-33524038-A-G		not specified	Uncertain significance (Feb 05, 2024)
2-33524042-A-G		not specified	Uncertain significance (Jan 05, 2022)
2-33524047-G-A		not specified	Uncertain significance (Sep 06, 2022)
2-33524505-G-A		not specified	Uncertain significance (Nov 03, 2022)
2-33527185-A-C		not specified	Uncertain significance (Oct 25, 2022)
2-33527186-A-G		not specified	Uncertain significance (Aug 08, 2022)
2-33527195-A-G		not specified	Uncertain significance (Jun 24, 2022)
2-33527206-G-A		not specified	Uncertain significance (Aug 12, 2022)
2-33527220-C-G		not specified	Uncertain significance (Oct 26, 2021)
2-33527232-C-A			Likely benign (Jul 01, 2022)
2-33534350-G-C		not specified	Uncertain significance (Aug 22, 2023)
2-33539176-C-A		not specified	Uncertain significance (Jan 04, 2022)
2-33543528-A-G		not specified	Uncertain significance (Jul 20, 2021)
2-33543599-G-A		not specified	Uncertain significance (Nov 03, 2023)
2-33549666-A-G		not specified	Uncertain significance (Feb 13, 2024)
2-33549709-G-T		not specified	Uncertain significance (Mar 05, 2024)
2-33549712-C-T			Likely benign (Aug 14, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASGRP3	protein_coding	protein_coding	ENST00000403687	16	128427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00911	0.991	124615	0	44	124659	0.000177

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.504	334	361	0.925	0.0000182	4536
Missense in Polyphen		133	151.05	0.8805		1985
Synonymous	0.315	131	136	0.966	0.00000709	1272
Loss of Function	3.72	10	33.1	0.302	0.00000152	432

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000223
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000268	0.000265
Middle Eastern	0.000226	0.000223
South Asian	0.0000334	0.0000327
Other	0.000500	0.000495

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for Ras and Rap1. {ECO:0000269|PubMed:10934204}.
• Pathway: B cell receptor signaling pathway - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Integrated Breast Cancer Pathway;B Cell Receptor Signaling Pathway;MAPK Signaling Pathway;Ras Signaling;Regulation of Ras family activation;Signal Transduction;Activation of RAS in B cells;Signaling by the B Cell Receptor (BCR);Immune System;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);BCR;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Intolerance Scores

• loftool: 0.685
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.576
• hipred: Y
• hipred_score: 0.605
• ghis: 0.496

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.818

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rasgrp3
• Phenotype: normal phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: MAPK cascade;small GTPase mediated signal transduction;Ras protein signal transduction;positive regulation of GTPase activity
• Cellular component: plasma membrane;integral component of plasma membrane;guanyl-nucleotide exchange factor complex;perinuclear region of cytoplasm
• Molecular function: guanyl-nucleotide exchange factor activity;Ras guanyl-nucleotide exchange factor activity;GTPase activator activity;calcium ion binding;protein binding;kinase binding;diacylglycerol binding