RBP1

protein-coding

retinol binding protein 1, the group of Fatty acid binding protein family

Gene summary

This gene encodes the carrier protein involved in the transport of retinol (vitamin A alcohol) from the liver storage site to peripheral tissue. Vitamin A is a fat-soluble vitamin necessary for growth, reproduction, differentiation of epithelial tissues, and vision. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

MANE transcript

NM_002899.5

Inheritance

—

ClinVar variants

U:96B:33

Top phenotype

RBP1-related condition

gnomAD constraint

pLI —, LoF o/e 0.99

Max pathogenic AF

—

Genomic locus

chr3:139,517,434-139,539,829

External References & Databases

Ensembl (ENSG00000114115)

Transcript & Mutation Effects

hg38 • Region Span ~22.4 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 RBP1 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 144

not specifiedTotal: 24

RBP1-related conditionTotal: 2

Leber congenital amaurosisTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002899.5. 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			2 clinvar	30 clinvar	2 clinvar	34
missense			83 clinvar		1 clinvar	84
nonsense			3 clinvar			3
start loss			2 clinvar			2
frameshift			6 clinvar			6
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	30	3	129

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002899.5	RefSeq	NP_002890.2	4	MANE Select
ENST00000672186.1	Ensembl	ENSP00000500931.1	4	MANE Select
NM_001130992.3	RefSeq	NP_001124464.1	3	Standard
NM_001130993.3	RefSeq	NP_001124465.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Retinoblastoma (RB) in Cancer
Vitamin A and Carotenoid Metabolism
Signaling by GPCR
Signal Transduction
Metabolism of fat-soluble vitamins

Biological Process

retinoid metabolic process
retinoic acid biosynthetic process
vitamin A metabolic process
lipid homeostasis

Molecular Function

retinoid binding
retinal binding
all-trans-retinol binding

Cellular Component

nucleoplasm
lipid droplet
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000232219
Coding exons: 4
Length: 22396
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.625	92	110	0.833	0.00000583	1298
Missense (PolyPhen)		42	46.419	0.90479		530
Synonymous	0.0149	43	43.1	0.997	0.00000231	364
Loss of Function	0.0370	8	8.11	0.986	3.47e-7	92

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00043	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00046	0.00040	rare
South Asian	0.00010	0.000098	rare
Other	0.00054	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cytoplasmic retinol-binding protein (PubMed:22665496, PubMed:26900151, PubMed:28057518). Accepts retinol from the transport protein STRA6, and thereby contributes to retinol uptake, storage and retinoid homeostasis (PubMed:15632377, PubMed:22665496). {ECO:0000269|PubMed:15632377, ECO:0000269|PubMed:22665496, ECO:0000269|PubMed:26900151, ECO:0000269|PubMed:28057518}.;

Recessive Scores

pRec: 0.322

Intolerance Scores

LoFtool: 0.858
RVIS EVS: 0.08
RVIS percentile EVS: 59.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.525

Gene Damage Prediction

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