RAP2B

protein-coding

RAP2B, member of RAS oncogene family, the group of RAS type GTPase family

Gene summary

This intronless gene belongs to a family of RAS-related genes. The proteins encoded by these genes share approximately 50% amino acid identity with the classical RAS proteins and have numerous structural features in common. The most striking difference between the RAP and RAS proteins resides in their 61st amino acid: glutamine in RAS is replaced by threonine in RAP proteins. Evidence suggests that this protein may be polyisoprenylated and palmitoylated. [provided by RefSeq, Jul 2008]

MANE transcript

NM_002886.4

Inheritance

—

ClinVar variants

U:13B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr3:153,162,226-153,170,627

External References & Databases

Ensembl (ENSG00000181467)

Transcript & Mutation Effects

hg38 • Region Span ~8.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAP2B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 13

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002886.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			13 clinvar			13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	1	0	14

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002886.4	RefSeq	NP_002877.2	1	MANE Select
ENST00000323534.5	Ensembl	ENSP00000319096.2	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
phospholipase c-epsilon pathway
Innate Immune System
Immune System

Biological Process

signal transduction
microvillus assembly
platelet activation
negative regulation of cell migration
positive regulation of protein autophosphorylation

Molecular Function

GTPase activity
protein binding
GTP binding
GDP binding
protein domain specific binding

Cellular Component

cytosol
plasma membrane
bicellular tight junction
membrane
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323534
Coding exons: 1
Length: 6237
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.25	41	106	0.385	0.00000482	1184
Missense (PolyPhen)		9	51.081	0.17619		579
Synonymous	-0.422	54	50.2	1.08	0.00000247	367
Loss of Function	1.87	1	5.92	0.169	2.55e-7	64

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Small GTP-binding protein which cycles between a GDP- bound inactive and a GTP-bound active form. Involved in EGFR and CHRM3 signaling pathways through stimulation of PLCE1. May play a role in cytoskeletal rearrangements and regulate cell spreading through activation of the effector TNIK. May regulate membrane vesiculation in red blood cells. {ECO:0000269|PubMed:11877431, ECO:0000269|PubMed:15143162, ECO:0000269|PubMed:16540189}.;

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.113
RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.823

Gene Damage Prediction

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