RBP2

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

Basic information

Region (hg38): 3:139452884-139480747

Links

ENSG00000114113 ∙ NCBI:5948 ∙ OMIM:180280 ∙ HGNC:9920 ∙ Uniprot:P50120 ∙ 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 RBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBP2 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in RBP2

This is a list of pathogenic ClinVar variants found in the RBP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-139462122-C-T		not specified	Uncertain significance (Jul 14, 2021)
3-139462147-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-139462188-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-139462245-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-139462257-C-T		not specified	Likely benign (Oct 22, 2021)
3-139462272-C-T		not specified	Uncertain significance (Feb 28, 2024)
3-139462287-A-G		not specified	Uncertain significance (Aug 17, 2021)
3-139476395-T-C		not specified	Uncertain significance (Mar 15, 2024)
3-139476414-T-G		not specified	Uncertain significance (Nov 18, 2022)
3-139476437-G-A		not specified	Uncertain significance (Jan 31, 2024)
3-139476448-G-C		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBP2	protein_coding	protein_coding	ENST00000232217	4	27864

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.221	0.746	125734	0	11	125745	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.377	71	80.5	0.882	0.00000474	901
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intracellular transport of retinol.
• Pathway: Vitamin digestion and absorption - Homo sapiens (human);Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;Metabolism of vitamins and cofactors;retinoate biosynthesis II;retinoate biosynthesis I;retinol biosynthesis;Retinoid metabolism and transport;G alpha (i) signalling events;Visual phototransduction;the visual cycle I (vertebrates);GPCR downstream signalling;Regulation of retinoblastoma protein (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.702
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.0486
• hipred: N
• hipred_score: 0.380
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbp2
• Phenotype: homeostasis/metabolism phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: retinoid metabolic process;vitamin A metabolic process;epidermis development
• Cellular component: cytosol
• Molecular function: retinoid binding;retinal binding;retinol binding