RAP1GAP2

RAP1 GTPase activating protein 2

Basic information

Region (hg38): 17:2755704-3037741

Previous symbols: [ "GARNL4" ]

Links

ENSG00000132359 ∙ NCBI:23108 ∙ OMIM:618714 ∙ HGNC:29176 ∙ Uniprot:Q684P5 ∙ 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 RAP1GAP2 gene.

• Inborn genetic diseases (27 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAP1GAP2 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			25	2	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	25	2	3

Variants in RAP1GAP2

This is a list of pathogenic ClinVar variants found in the RAP1GAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-2905313-C-T		not specified	Likely benign (Mar 02, 2023)
17-2905331-C-T		not specified	Uncertain significance (Aug 13, 2021)
17-2963433-G-A		not specified	Uncertain significance (Oct 29, 2021)
17-2963445-T-C		not specified	Uncertain significance (Dec 13, 2023)
17-2963908-G-A		not specified	Uncertain significance (Oct 12, 2021)
17-2963919-G-A		not specified	Uncertain significance (Jun 02, 2023)
17-2963938-G-A		not specified	Uncertain significance (Jul 26, 2021)
17-2963949-T-C		not specified	Uncertain significance (Jun 03, 2022)
17-2965594-G-A		not specified	Likely benign (Oct 12, 2021)
17-2980303-G-A		not specified	Uncertain significance (Nov 17, 2023)
17-2980313-G-A			Benign (Apr 30, 2018)
17-2981229-A-G		not specified	Uncertain significance (May 10, 2022)
17-2981247-A-G		not specified	Uncertain significance (Nov 05, 2021)
17-2995362-C-G		not specified	Uncertain significance (Jan 02, 2024)
17-2995425-G-A		not specified	Uncertain significance (Dec 02, 2021)
17-2998300-T-C		not specified	Uncertain significance (Jan 04, 2022)
17-2998316-C-A		not specified	Uncertain significance (Jul 06, 2021)
17-2998335-G-A		not specified	Uncertain significance (Oct 28, 2023)
17-3005385-G-A		not specified	Uncertain significance (Nov 09, 2022)
17-3005429-G-A		not specified	Uncertain significance (Dec 08, 2021)
17-3005959-C-T		not specified	Uncertain significance (Dec 07, 2023)
17-3006006-G-T		not specified	Uncertain significance (Jan 05, 2022)
17-3006030-G-A		not specified	Uncertain significance (Mar 12, 2024)
17-3008048-A-G		not specified	Uncertain significance (Jan 26, 2023)
17-3008058-C-G		not specified	Uncertain significance (Sep 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAP1GAP2	protein_coding	protein_coding	ENST00000254695	24	260684

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0307	124625	0	14	124639	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	307	438	0.701	0.0000270	4768
Missense in Polyphen		66	107.89	0.61175		1131
Synonymous	0.784	168	181	0.926	0.0000125	1370
Loss of Function	4.97	7	41.6	0.168	0.00000204	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000453	0.0000442
Middle Eastern	0.000114	0.000111
South Asian	0.0000359	0.0000327
Other	0.000333	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activator for the nuclear Ras-related regulatory protein RAP-1A (KREV-1), converting it to the putatively inactive GDP-bound state. {ECO:0000269|PubMed:15632203}.
• Pathway: Immune System;Rap1 signalling;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.128
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.51

Haploinsufficiency Scores

• pHI: 0.472
• hipred: Y
• hipred_score: 0.792
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rap1gap2

Gene ontology

• Biological process: regulation of cell size;negative regulation of neuron projection development;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: centrosome;cytosol;plasma membrane;nuclear membrane;neuron projection;perinuclear region of cytoplasm
• Molecular function: GTPase activator activity;protein binding