RBP2

protein-coding

retinol binding protein 2, the group of Fatty acid binding protein family

Gene summary

This gene encodes an abundant protein present in the small intestinal epithelium. It is thought to participate in the uptake and/or intracellular metabolism of vitamin A. Vitamin A is a fat-soluble vitamin necessary for growth, reproduction, differentiation of epithelial tissues, and vision. This protein may also modulate the supply of retinoic acid to the nuclei of endometrial cells during the menstrual cycle. [provided by RefSeq, Aug 2015]

MANE transcript

NM_004164.3

Inheritance

—

ClinVar variants

U:20B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr3:139,452,884-139,480,747

External References & Databases

Ensembl (ENSG00000114113)

Transcript & Mutation Effects

hg38 • Region Span ~27.9 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 RBP2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004164.3. 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						0
missense			19 clinvar	1 clinvar		20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	20	1	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004164.3	RefSeq	NP_004155.2	4	MANE Select
ENST00000232217.6	Ensembl	ENSP00000232217.2	4	MANE Select
ENST00000506825.1	Ensembl	ENSP00000421266.1	1	Standard
ENST00000511956.1	Ensembl	ENSP00000424333.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin digestion and absorption - Homo sapiens (human)
Vitamin A and Carotenoid Metabolism
Signaling by GPCR
Signal Transduction
Metabolism of fat-soluble vitamins

Biological Process

retinoid metabolic process
vitamin A metabolic process
epidermis development

Molecular Function

retinoid binding
retinal binding
retinol binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000232217
Coding exons: 4
Length: 27864
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125745
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.377	71	80.5	0.882	0.00000474	901
Missense (PolyPhen)		31	25.556	1.213		287
Synonymous	1.26	19	27.4	0.695	0.00000143	230
Loss of Function	1.78	2	7.12	0.281	3.03e-7	82

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	0.00027	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Intracellular transport of retinol.;

Recessive Scores

pRec: 0.121

Intolerance Scores

LoFtool: 0.702
RVIS EVS: -0.16
RVIS percentile EVS: 41.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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