RASGEF1C

RasGEF domain family member 1C

Basic information

Region (hg38): 5:180100795-180209211

Links

ENSG00000146090 ∙ NCBI:255426 ∙ ∙ HGNC:27400 ∙ Uniprot:Q8N431 ∙ 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 RASGEF1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RASGEF1C 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			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	0	0

Variants in RASGEF1C

This is a list of pathogenic ClinVar variants found in the RASGEF1C region.

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

Position	Type	Phenotype	Significance	ClinVar
5-180102123-C-T		not specified	Uncertain significance (Dec 31, 2024)
5-180102143-C-T		not specified	Uncertain significance (Mar 29, 2023)
5-180111499-T-C		not specified	Uncertain significance (Dec 16, 2023)
5-180111506-G-C		not specified	Uncertain significance (May 13, 2024)
5-180111569-C-G		not specified	Uncertain significance (Feb 13, 2025)
5-180114481-C-T		not specified	Uncertain significance (Nov 13, 2024)
5-180114487-C-T		not specified	Uncertain significance (Feb 19, 2025)
5-180118641-G-A		not specified	Uncertain significance (Oct 25, 2022)
5-180118649-G-A		not specified	Uncertain significance (Feb 21, 2024)
5-180118688-G-A		not specified	Uncertain significance (May 25, 2022)
5-180119360-A-G		not specified	Uncertain significance (Mar 11, 2025)
5-180119376-C-T		not specified	Uncertain significance (Jan 23, 2023)
5-180119382-T-C		not specified	Uncertain significance (Dec 26, 2023)
5-180119394-G-A		not specified	Uncertain significance (Oct 17, 2023)
5-180121088-C-A		not specified	Uncertain significance (Nov 21, 2024)
5-180121140-T-C		not specified	Uncertain significance (Apr 29, 2024)
5-180127622-A-C		not specified	Uncertain significance (Sep 20, 2023)
5-180127673-C-T		not specified	Uncertain significance (Jul 30, 2023)
5-180127674-G-A		not specified	Uncertain significance (Oct 20, 2023)
5-180128418-C-T		not specified	Uncertain significance (Jun 30, 2024)
5-180128430-G-C		not specified	Uncertain significance (Feb 03, 2022)
5-180128435-G-A		not specified	Uncertain significance (Nov 09, 2021)
5-180128436-C-A		not specified	Uncertain significance (Dec 28, 2022)
5-180128451-C-T		not specified	Uncertain significance (Jul 20, 2021)
5-180128549-C-T		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RASGEF1C	protein_coding	protein_coding	ENST00000393371	13	108359

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000961	0.986	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	197	277	0.712	0.0000168	3042
Missense in Polyphen		39	67.165	0.58066		803
Synonymous	0.480	112	119	0.944	0.00000781	903
Loss of Function	2.21	12	23.6	0.508	0.00000101	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.632
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.3

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.682
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rasgef1c

Gene ontology

• Biological process: small GTPase mediated signal transduction
• Molecular function: guanyl-nucleotide exchange factor activity