RASAL1

RAS protein activator like 1, the group of Pleckstrin homology domain containing|C2 and RasGAP domain containing

Basic information

Region (hg38): 12:113098819-113136239

Links

ENSG00000111344 ∙ NCBI:8437 ∙ OMIM:604118 ∙ HGNC:9873 ∙ Uniprot:O95294 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• breast cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RASAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASAL1 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				5	4	9
missense			56	8	2	66
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1		1
Total	0	0	57	14	6

Variants in RASAL1

This is a list of pathogenic ClinVar variants found in the RASAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113099954-G-A			Likely benign (May 09, 2018)
12-113099994-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-113100024-G-A		not specified	Uncertain significance (May 04, 2022)
12-113100045-G-A		not specified	Uncertain significance (Oct 06, 2024)
12-113100059-G-A		not specified	Uncertain significance (Jan 26, 2022)
12-113101882-C-T			Likely benign (Aug 15, 2017)
12-113101901-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-113101902-G-A		not specified	Uncertain significance (May 05, 2023)
12-113101902-G-C		not specified	Uncertain significance (Nov 19, 2022)
12-113101910-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-113101991-G-A		not specified	Uncertain significance (Feb 26, 2024)
12-113102004-C-G		not specified	Uncertain significance (Feb 15, 2023)
12-113102007-C-T		not specified	Uncertain significance (May 27, 2022)
12-113102008-G-A			Benign (Dec 31, 2019)
12-113103960-T-C		not specified	Uncertain significance (Jul 13, 2021)
12-113103981-G-A		not specified	Uncertain significance (May 31, 2023)
12-113104005-C-G		not specified	Uncertain significance (Dec 02, 2021)
12-113104014-A-G		not specified	Uncertain significance (Apr 12, 2024)
12-113104048-A-C		not specified	Uncertain significance (Dec 01, 2022)
12-113104177-G-A		not specified	Uncertain significance (Mar 30, 2024)
12-113104216-T-TG			Uncertain significance (Jul 01, 2022)
12-113104228-G-A		not specified	Uncertain significance (Oct 06, 2021)
12-113104252-A-G		not specified	Uncertain significance (Nov 07, 2022)
12-113105734-A-T		not specified	Uncertain significance (May 12, 2024)
12-113105737-A-G		not specified	Benign/Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASAL1	protein_coding	protein_coding	ENST00000546530	21	37421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.21e-14	0.708	125654	0	94	125748	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.757	420	466	0.901	0.0000283	5158
Missense in Polyphen		145	162.82	0.89055		1796
Synonymous	1.57	159	186	0.854	0.0000104	1649
Loss of Function	1.79	28	40.3	0.695	0.00000204	449

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000431
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000829	0.000816
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000296	0.000290
Middle Eastern	0.000829	0.000816
South Asian	0.000953	0.000948
Other	0.000354	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable inhibitory regulator of the Ras-cyclic AMP pathway (PubMed:9751798). Plays a role in dendrite formation by melanocytes (PubMed:23999003). {ECO:0000269|PubMed:23999003, ECO:0000269|PubMed:9751798}.
• Pathway: Ras signaling pathway - Homo sapiens (human);Ras Signaling;Regulation of Ras family activation;Signal Transduction;Regulation of RAS by GAPs;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.0953

Intolerance Scores

• loftool: 0.862
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.85

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.589
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasal1

Gene ontology

• Biological process: MAPK cascade;signal transduction;positive regulation of GTPase activity;negative regulation of Ras protein signal transduction;cellular response to calcium ion;positive regulation of dendrite extension
• Cellular component: cytosol;plasma membrane
• Molecular function: GTPase activator activity;phospholipid binding;metal ion binding