RASGEF1A

RasGEF domain family member 1A

Basic information

Region (hg38): 10:43194535-43267065

Links

ENSG00000198915 ∙ NCBI:221002 ∙ OMIM:614531 ∙ HGNC:24246 ∙ Uniprot:Q8N9B8 ∙ 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 RASGEF1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASGEF1A 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in RASGEF1A

This is a list of pathogenic ClinVar variants found in the RASGEF1A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-43197043-C-G		not specified	Uncertain significance (May 30, 2024)
10-43197048-C-A		not specified	Uncertain significance (Apr 01, 2024)
10-43198035-T-C		not specified	Uncertain significance (Mar 26, 2024)
10-43198061-G-C		not specified	Uncertain significance (Jul 27, 2022)
10-43198072-C-G		not specified	Uncertain significance (Oct 25, 2023)
10-43198072-C-T		not specified	Uncertain significance (Jun 06, 2023)
10-43198096-C-T		not specified	Uncertain significance (Aug 31, 2023)
10-43198107-C-G		not specified	Uncertain significance (Feb 28, 2024)
10-43199177-G-T		not specified	Uncertain significance (Sep 22, 2022)
10-43200223-T-A		not specified	Uncertain significance (Feb 28, 2023)
10-43200678-G-C		not specified	Uncertain significance (Jul 25, 2023)
10-43200717-C-T		not specified	Uncertain significance (Aug 06, 2021)
10-43200752-G-C		not specified	Uncertain significance (Jul 06, 2021)
10-43200777-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-43200788-C-T		not specified	Uncertain significance (Apr 29, 2024)
10-43200845-C-T		not specified	Uncertain significance (May 15, 2024)
10-43201828-G-A		not specified	Uncertain significance (Mar 02, 2023)
10-43201915-C-T		not specified	Uncertain significance (Oct 06, 2023)
10-43205938-G-A		not specified	Uncertain significance (May 18, 2023)
10-43205987-G-A		not specified	Uncertain significance (Jun 01, 2023)
10-43206029-C-T		not specified	Uncertain significance (Jan 30, 2024)
10-43206053-G-C		not specified	Uncertain significance (Jan 23, 2024)
10-43206065-C-T		not specified	Uncertain significance (Dec 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASGEF1A	protein_coding	protein_coding	ENST00000395809	12	72385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.974	0.0256	125709	0	6	125715	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	160	287	0.558	0.0000165	3200
Missense in Polyphen		16	60.443	0.26471		748
Synonymous	0.131	117	119	0.985	0.00000755	886
Loss of Function	4.03	3	24.5	0.122	0.00000121	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) with specificity for RAP2A, KRAS, HRAS, and NRAS (in vitro). Plays a role in cell migration. {ECO:0000269|PubMed:17121879, ECO:0000269|PubMed:19645719}.
• Pathway: Integrated Breast Cancer Pathway;Signal Transduction;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.224
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.282
• hipred: Y
• hipred_score: 0.745
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasgef1a

Gene ontology

• Biological process: MAPK cascade;small GTPase mediated signal transduction;cell migration;positive regulation of Ras protein signal transduction
• Cellular component: cytosol
• Molecular function: Ras guanyl-nucleotide exchange factor activity