RASA3

RAS p21 protein activator 3, the group of C2 and RasGAP domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 13:113977783-114132623

Links

ENSG00000185989 ∙ NCBI:22821 ∙ OMIM:605182 ∙ HGNC:20331 ∙ Uniprot:Q14644 ∙ 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 RASA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASA3 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				2	3	5
missense			58	3		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	5	3

Variants in RASA3

This is a list of pathogenic ClinVar variants found in the RASA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-113979375-T-C		not specified	Uncertain significance (May 25, 2022)
13-113979389-G-T		not specified	Uncertain significance (Jan 10, 2022)
13-113979409-C-T		not specified	Uncertain significance (Nov 09, 2022)
13-113979413-G-A			Benign (May 21, 2018)
13-113981721-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-113981751-C-T		not specified	Uncertain significance (Jul 12, 2022)
13-113981776-G-A			Likely benign (Jun 01, 2022)
13-113981802-A-C		not specified	Uncertain significance (Nov 10, 2022)
13-113981810-T-C		not specified	Uncertain significance (Apr 22, 2022)
13-113992509-T-C		not specified	Uncertain significance (Mar 01, 2023)
13-113992524-G-A		not specified	Uncertain significance (Dec 12, 2023)
13-113992541-G-A		not specified	Uncertain significance (May 06, 2024)
13-113992563-C-T		not specified	Uncertain significance (Jun 21, 2023)
13-113996619-C-T		not specified	Uncertain significance (May 02, 2024)
13-113996627-C-T		not specified	Uncertain significance (Oct 05, 2023)
13-113996660-A-G		not specified	Uncertain significance (Jun 29, 2022)
13-113996668-C-A		not specified	Uncertain significance (Nov 17, 2023)
13-113996692-G-T		not specified	Uncertain significance (Aug 30, 2021)
13-113996703-T-C		not specified	Uncertain significance (Mar 31, 2024)
13-113999606-C-T			Likely benign (Jun 01, 2022)
13-113999614-G-C		not specified	Uncertain significance (Aug 17, 2021)
13-113999658-G-C		not specified	Uncertain significance (Jun 07, 2024)
13-113999659-G-A		not specified	Uncertain significance (Oct 26, 2022)
13-114007543-G-C		not specified	Uncertain significance (Feb 16, 2023)
13-114007563-C-T		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASA3	protein_coding	protein_coding	ENST00000334062	24	150893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.91e-10	1.00	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.68	416	524	0.793	0.0000342	5510
Missense in Polyphen		192	254.78	0.7536		2597
Synonymous	-2.01	270	231	1.17	0.0000175	1524
Loss of Function	3.16	24	47.5	0.505	0.00000228	564

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000500	0.000499
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000218	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.0000980	0.0000980
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitory regulator of the Ras-cyclic AMP pathway. Binds inositol tetrakisphosphate (IP4) with high affinity. Might be a specific IP4 receptor.
• Pathway: Ras signaling pathway - Homo sapiens (human);MAPK Cascade;Ras Signaling;Signal Transduction;Regulation of RAS by GAPs;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.191
• rvis_EVS: -1.66
• rvis_percentile_EVS: 2.74

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.603
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasa3
• Phenotype: immune system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); reproductive system phenotype; embryo phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: rasa3
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: MAPK cascade;signal transduction;positive regulation of GTPase activity;negative regulation of Ras protein signal transduction;release of sequestered calcium ion into cytosol
• Cellular component: cytosol;intrinsic component of the cytoplasmic side of the plasma membrane
• Molecular function: GTPase activator activity;calcium-release channel activity;metal ion binding