RBP5

protein-coding

retinol binding protein 5, the group of Fatty acid binding protein family

Gene summary

The protein encoded by this gene is a cellular retinol-binding protein expressed highly in kidney and liver. Down-regulation of the encoded protein in hepatocellular carcinoma was associated with large tumor size and poor patient survival rates. [provided by RefSeq, Jul 2016]

MANE transcript

NM_031491.4

Inheritance

—

ClinVar variants

U:31B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr12:7,115,736-7,128,889

External References & Databases

Ensembl (ENSG00000139194)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 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 RBP5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031491.4. 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 clinvar		2
missense			29 clinvar	1 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	31	2	0	33

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031491.4	RefSeq	NP_113679.1	4	MANE Select
ENST00000266560.8	Ensembl	ENSP00000266560.3	4	MANE Select
NM_001329454.2	RefSeq	NP_001316383.1	3	Standard
ENST00000542370.1	Ensembl	ENSP00000438083.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

retinoate biosynthesis II
retinoate biosynthesis I
retinol biosynthesis
the visual cycle I (vertebrates)

Molecular Function

retinoid binding
protein binding
retinal binding
retinol binding

Cellular Component

cytoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266560
Coding exons: 4
Length: 5259
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125747
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.402	70	80.1	0.874	0.00000481	866
Missense (PolyPhen)		21	29.957	0.70101		331
Synonymous	1.57	22	33.6	0.655	0.00000220	248
Loss of Function	0.350	7	8.07	0.867	5.23e-7	75

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00043	0.00042	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Intracellular transport of retinol. {ECO:0000269|PubMed:11274389}.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.676
RVIS EVS: 1.06
RVIS percentile EVS: 91.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.460

Gene Damage Prediction

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