RAP2C

RAP2C, member of RAS oncogene family, the group of RAS type GTPase family

Basic information

Region (hg38): X:132203024-132219480

Links

ENSG00000123728 ∙ NCBI:57826 ∙ OMIM:301016 ∙ HGNC:21165 ∙ Uniprot:Q9Y3L5 ∙ 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 RAP2C gene.

• not_specified (6 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAP2C gene is commonly pathogenic or not. These statistics are base on transcript: NM_001271186.2. 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				1	1	2
missense			6			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	1	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAP2C	protein_coding	protein_coding	ENST00000342983	2	16419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.296	0.631	124648	0	1	124649	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	23	61.0	0.377	0.00000416	1196
Missense in Polyphen		7	21.825	0.32073		467
Synonymous	-1.07	31	24.3	1.28	0.00000182	356
Loss of Function	1.37	1	3.94	0.254	2.47e-7	91

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)	0.0000123	0.00000889
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. May play a role in cytoskeletal rearrangements and regulate cell spreading through activation of the effector TNIK. May play a role in SRE-mediated gene transcription. {ECO:0000269|PubMed:17447155}.
• Pathway: Tight junction - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.177
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.612
• hipred: N
• hipred_score: 0.483
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rap2c

Gene ontology

• Biological process: microvillus assembly;negative regulation of cell migration;positive regulation of protein autophosphorylation;Rap protein signal transduction;neutrophil degranulation;regulation of protein tyrosine kinase activity;establishment of endothelial intestinal barrier;positive regulation of nucleic acid-templated transcription
• Cellular component: cytoplasm;cytosol;plasma membrane;bicellular tight junction;cell-cell contact zone;recycling endosome membrane;extracellular exosome;tertiary granule membrane
• Molecular function: transcription coactivator activity;GTPase activity;protein binding;GTP binding;GDP binding