RABGAP1

RAB GTPase activating protein 1

Basic information

Region (hg38): 9:122940833-123104866

Links

ENSG00000011454 ∙ NCBI:23637 ∙ OMIM:615882 ∙ HGNC:17155 ∙ Uniprot:Q9Y3P9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RABGAP1 gene.

• not_specified (130 variants)
• not_provided (5 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RABGAP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012197.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			83	3		86
nonsense	1					1
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)						0
Total	1	0	85	3	0

Highest pathogenic variant AF is 6.8418547e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RABGAP1	protein_coding	protein_coding	ENST00000373647	25	164034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.11e-9	125596	0	3	125599	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.96	368	566	0.650	0.0000303	7063
Missense in Polyphen		145	289.37	0.50109		3570
Synonymous	0.408	201	208	0.964	0.0000112	1967
Loss of Function	7.12	1	61.1	0.0164	0.00000318	759

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a GTPase-activating protein of RAB6A. May play a role in microtubule nucleation by centrosome. May participate in a RAB6A-mediated pathway involved in the metaphase- anaphase transition. {ECO:0000269|PubMed:10202141, ECO:0000269|PubMed:16395330}.
• Pathway: Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.265
• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.5

Haploinsufficiency Scores

• pHI: 0.292
• hipred: Y
• hipred_score: 0.685
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rabgap1

Gene ontology

• Biological process: intracellular protein transport;cell cycle;regulation of GTPase activity;activation of GTPase activity;regulation of cilium assembly
• Cellular component: centrosome;cytosol;microtubule associated complex
• Molecular function: GTPase activator activity;protein binding;tubulin binding;Rab GTPase binding