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.

not_specified (114 variants)
not_provided (5 variants)
Short_stature (2 variants)

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. These statistics are base on transcript: NM_000007368.4. 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				5 clinvar	3 clinvar	8
missense		1 clinvar	108 clinvar	3 clinvar		112
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	1	108	8	3

Highest pathogenic variant AF is 0.0000225812

Loading clinvar variants...

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