RAP1GAP

RAP1 GTPase activating protein

Basic information

Region (hg38): 1:21596221-21669357

Previous symbols: [ "RAP1GA1" ]

Links

ENSG00000076864 ∙ NCBI:5909 ∙ OMIM:600278 ∙ HGNC:9858 ∙ Uniprot:P47736 ∙ 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 RAP1GAP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAP1GAP 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			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in RAP1GAP

This is a list of pathogenic ClinVar variants found in the RAP1GAP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-21598016-G-A		not specified	Uncertain significance (Aug 16, 2022)
1-21598035-C-T		not specified	Uncertain significance (Oct 05, 2023)
1-21598474-T-C		not specified	Uncertain significance (May 01, 2022)
1-21598476-G-A			Likely benign (Jun 01, 2022)
1-21598478-G-T		not specified	Uncertain significance (Dec 15, 2022)
1-21598495-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-21599505-C-G		not specified	Uncertain significance (Apr 12, 2023)
1-21599516-A-C		not specified	Uncertain significance (May 24, 2023)
1-21599538-C-T		not specified	Uncertain significance (Feb 17, 2024)
1-21599588-G-A		not specified	Likely benign (Jan 20, 2023)
1-21599595-C-G		not specified	Uncertain significance (Apr 08, 2024)
1-21601735-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-21602826-T-C		not specified	Uncertain significance (Jun 21, 2022)
1-21608322-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-21608896-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-21608909-T-C		not specified	Uncertain significance (Sep 26, 2023)
1-21609594-T-G		not specified	Uncertain significance (Sep 10, 2021)
1-21609645-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-21611777-G-T		not specified	Uncertain significance (Aug 17, 2022)
1-21611788-T-A		not specified	Uncertain significance (Mar 31, 2024)
1-21612042-T-C		not specified	Uncertain significance (Aug 12, 2021)
1-21612069-C-G		not specified	Uncertain significance (Jan 31, 2024)
1-21613190-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-21613998-C-T		not specified	Uncertain significance (Jun 18, 2024)
1-21614026-C-T		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAP1GAP	protein_coding	protein_coding	ENST00000290101	24	73094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.844	0.156	125729	0	16	125745	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	308	444	0.693	0.0000277	4714
Missense in Polyphen		92	159.35	0.57736		1683
Synonymous	-0.370	201	194	1.03	0.0000144	1357
Loss of Function	4.80	8	41.3	0.194	0.00000194	498

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.000289	0.000277
European (Non-Finnish)	0.0000444	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000367	0.0000327
Other	0.00	0.00

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:15141215}.
• Pathway: Rap1 signaling pathway - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway;Splicing factor NOVA regulated synaptic proteins;Developmental Biology;Immune System;Rap1 signalling;Adaptive Immune System;RET signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.158

Intolerance Scores

• loftool: 0.0176
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.24

Haploinsufficiency Scores

• pHI: 0.374
• hipred: Y
• hipred_score: 0.774
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.863

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rap1gap

Gene ontology

• Biological process: signal transduction;axon guidance;regulation of GTPase activity;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction;negative regulation of microvillus assembly
• Cellular component: Golgi membrane;cytosol;membrane
• Molecular function: GTPase activity;GTPase activator activity;protein binding;Ras GTPase binding;protein homodimerization activity