RASGEF1B

RasGEF domain family member 1B

Basic information

Region (hg38): 4:81426392-82044244

Links

ENSG00000138670 ∙ NCBI:153020 ∙ OMIM:614532 ∙ HGNC:24881 ∙ Uniprot:Q0VAM2 ∙ 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 RASGEF1B gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASGEF1B 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					1	1
missense			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	1

Variants in RASGEF1B

This is a list of pathogenic ClinVar variants found in the RASGEF1B region.

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

Position	Type	Phenotype	Significance	ClinVar
4-81433911-A-G		not specified	Uncertain significance (Jan 18, 2022)
4-81434650-C-T		RASGEF1B-related disorder	Benign (Feb 14, 2020)
4-81434665-G-A		not specified	Uncertain significance (May 27, 2022)
4-81434668-G-A		not specified	Uncertain significance (Jun 21, 2023)
4-81434680-C-A		not specified	Uncertain significance (Jan 06, 2023)
4-81440901-T-C		RASGEF1B-related disorder	Likely benign (Feb 27, 2019)
4-81440911-T-C		not specified	Uncertain significance (Mar 24, 2023)
4-81442336-A-C		RASGEF1B-related disorder	Benign (Apr 09, 2019)
4-81445574-G-A		not specified	Uncertain significance (Dec 20, 2022)
4-81445601-T-C		not specified	Uncertain significance (Jan 30, 2024)
4-81445609-C-T		not specified	Uncertain significance (Apr 11, 2023)
4-81445634-C-T		RASGEF1B-related disorder	Benign (Oct 29, 2019)
4-81445805-A-C		not specified	Uncertain significance (Dec 09, 2023)
4-81445823-G-A		not specified	Uncertain significance (Aug 02, 2022)
4-81447569-T-C		RASGEF1B-related disorder	Benign (Sep 17, 2019)
4-81447575-T-C		not specified	Uncertain significance (May 26, 2022)
4-81448076-A-G		not specified	Uncertain significance (Nov 03, 2022)
4-81448110-C-T		not specified	Uncertain significance (Sep 27, 2021)
4-81448112-T-C		not specified	Likely benign (Dec 02, 2022)
4-81448126-G-C		not specified	Uncertain significance (Mar 17, 2023)
4-81448247-C-T		not specified	Uncertain significance (Jan 03, 2024)
4-81448265-A-T		not specified	Uncertain significance (Aug 12, 2021)
4-81448266-C-A		not specified	Uncertain significance (Aug 12, 2021)
4-81457558-C-A		not specified	Uncertain significance (Dec 20, 2023)
4-81459339-T-C		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASGEF1B	protein_coding	protein_coding	ENST00000264400	13	617851

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.921	0.0793	125734	0	12	125746	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	199	267	0.746	0.0000146	3160
Missense in Polyphen		29	60.168	0.48199		736
Synonymous	0.197	90	92.4	0.974	0.00000521	834
Loss of Function	4.24	5	30.2	0.166	0.00000174	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000911	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) with specificity for RAP2A, it doesn't seems to activate other Ras family proteins (in vitro). {ECO:0000269|PubMed:19645719, ECO:0000269|PubMed:23894443}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.647
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.620
• hipred: Y
• hipred_score: 0.659
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasgef1b

Gene ontology

• Biological process: small GTPase mediated signal transduction;positive regulation of GTPase activity
• Cellular component: early endosome;late endosome;midbody
• Molecular function: Ras guanyl-nucleotide exchange factor activity