RASAL3

RAS protein activator like 3, the group of C2 and RasGAP domain containing

Basic information

Region (hg38): 19:15451624-15464544

Links

ENSG00000105122 ∙ NCBI:64926 ∙ OMIM:616561 ∙ HGNC:26129 ∙ Uniprot:Q86YV0 ∙ 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 RASAL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASAL3 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						0
missense			78	4	1	83
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	78	4	1

Variants in RASAL3

This is a list of pathogenic ClinVar variants found in the RASAL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-15451804-G-T		not specified	Uncertain significance (May 24, 2023)
19-15451808-C-T		not specified	Uncertain significance (Apr 15, 2024)
19-15451832-G-A		not specified	Uncertain significance (May 22, 2024)
19-15451838-G-A		not specified	Uncertain significance (Jul 27, 2024)
19-15451853-C-G		not specified	Uncertain significance (Sep 25, 2024)
19-15451887-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-15451890-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-15451913-C-G		not specified	Uncertain significance (Aug 17, 2021)
19-15452065-C-T		not specified	Uncertain significance (Feb 28, 2025)
19-15452073-C-A		not specified	Likely benign (Oct 28, 2024)
19-15452081-G-C		not specified	Uncertain significance (Jul 26, 2024)
19-15452659-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-15452676-T-C		not specified	Uncertain significance (Jun 18, 2021)
19-15452680-G-C		not specified	Uncertain significance (Feb 25, 2025)
19-15452704-G-C		not specified	Uncertain significance (Aug 27, 2024)
19-15452727-C-G		not specified	Uncertain significance (Oct 25, 2023)
19-15452790-G-C		not specified	Uncertain significance (Jan 20, 2025)
19-15453146-G-C		not specified	Uncertain significance (Aug 30, 2021)
19-15453162-A-T		not specified	Uncertain significance (Dec 10, 2024)
19-15453228-G-A		not specified	Uncertain significance (Jan 20, 2025)
19-15453237-G-C		not specified	Uncertain significance (Sep 29, 2023)
19-15453258-C-A		not specified	Uncertain significance (Mar 01, 2024)
19-15453298-G-C		not specified	Uncertain significance (Dec 28, 2023)
19-15453306-C-T		not specified	Uncertain significance (May 14, 2024)
19-15453310-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASAL3	protein_coding	protein_coding	ENST00000343625	17	12948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.11e-10	0.996	124565	0	116	124681	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	434	539	0.806	0.0000326	6272
Missense in Polyphen		118	165.87	0.7114		2006
Synonymous	2.19	181	222	0.814	0.0000127	2234
Loss of Function	2.68	23	41.7	0.552	0.00000239	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000227
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000167
Finnish	0.00248	0.00237
European (Non-Finnish)	0.000422	0.000416
Middle Eastern	0.000169	0.000167
South Asian	0.000368	0.000131
Other	0.00119	0.00116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a Ras GTPase-activating protein. Plays an important role in the expansion and functions of natural killer T (NKT) cells in the liver by negatively regulating RAS activity and the down-stream ERK signaling pathway. {ECO:0000250|UniProtKB:Q8C2K5}.
• Pathway: Ras signaling pathway - Homo sapiens (human);Ras Signaling;Signal Transduction;Regulation of RAS by GAPs;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Intolerance Scores

• loftool: 0.491
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.348
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasal3
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: MAPK cascade;positive regulation of GTPase activity;negative regulation of Ras protein signal transduction;positive regulation of NK T cell proliferation
• Cellular component: cytoplasm;cytosol;cell cortex;membrane;extracellular exosome;cytoplasmic side of membrane
• Molecular function: GTPase activator activity