RAP2A

RAP2A, member of RAS oncogene family, the group of RAS type GTPase family

Basic information

Region (hg38): 13:97434169-97469128

Previous symbols: [ "RAP2" ]

Links

ENSG00000125249 ∙ NCBI:5911 ∙ OMIM:179540 ∙ HGNC:9861 ∙ Uniprot:P10114 ∙ 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 RAP2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAP2A 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in RAP2A

This is a list of pathogenic ClinVar variants found in the RAP2A region.

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

Position	Type	Phenotype	Significance	ClinVar
13-97434475-G-A		not specified	Uncertain significance (May 18, 2022)
13-97434546-G-C		not specified	Uncertain significance (Jun 17, 2024)
13-97434558-G-C		not specified	Uncertain significance (Jun 17, 2024)
13-97434612-T-G		not specified	Uncertain significance (Nov 09, 2024)
13-97434711-G-A		not specified	Uncertain significance (Apr 09, 2024)
13-97464207-A-G		not specified	Uncertain significance (Jul 31, 2024)
13-97464234-G-C		not specified	Uncertain significance (Oct 01, 2024)
13-97464387-A-G		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAP2A	protein_coding	protein_coding	ENST00000245304	2	34907

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.851	0.147	125540	0	1	125541	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	34	109	0.311	0.00000509	1208
Missense in Polyphen		10	47.817	0.20913		550
Synonymous	-1.04	57	47.9	1.19	0.00000260	355
Loss of Function	2.32	0	6.24	0.00	2.66e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Small GTP-binding protein which cycles between a GDP- bound inactive and a GTP-bound active form. In its active form interacts with and regulates several effectors including MAP4K4, MINK1 and TNIK. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. More generally, it is part of several signaling cascades and may regulate cytoskeletal rearrangements, cell migration, cell adhesion and cell spreading. {ECO:0000269|PubMed:14966141, ECO:0000269|PubMed:15342639, ECO:0000269|PubMed:16246175, ECO:0000269|PubMed:16540189, ECO:0000269|PubMed:18930710, ECO:0000269|PubMed:20159449}.

Recessive Scores

• pRec: 0.190

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.800
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rap2a

Gene ontology

• Biological process: positive regulation of protein phosphorylation;microvillus assembly;negative regulation of cell migration;actin cytoskeleton reorganization;positive regulation of protein autophosphorylation;Rap protein signal transduction;cellular protein localization;cellular response to drug;establishment of protein localization;establishment of epithelial cell apical/basal polarity;regulation of JNK cascade;regulation of dendrite morphogenesis;protein localization to plasma membrane
• Cellular component: cytosol;plasma membrane;midbody;recycling endosome;recycling endosome membrane
• Molecular function: magnesium ion binding;GTPase activity;protein binding;GTP binding;GDP binding