RBP1

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

Basic information

Region (hg38): 3:139517434-139539829

Links

ENSG00000114115 ∙ NCBI:5947 ∙ OMIM:180260 ∙ HGNC:9919 ∙ Uniprot:P09455 ∙ 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 RBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBP1 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				21	3	24
missense			62		1	63
nonsense			2			2
start loss			3			3
frameshift			4			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			4	1		5
non coding			4	12	2	18
Total	0	0	76	33	6

Variants in RBP1

This is a list of pathogenic ClinVar variants found in the RBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-139517629-A-T			Uncertain significance (Dec 11, 2023)
3-139517634-A-T			Uncertain significance (Mar 11, 2022)
3-139517659-C-A		not specified	Uncertain significance (Jan 30, 2024)
3-139517664-C-G			Uncertain significance (Jan 11, 2024)
3-139517698-G-A			Likely benign (Nov 01, 2022)
3-139518401-G-C			Likely benign (Jan 06, 2024)
3-139518416-C-A			Uncertain significance (Aug 28, 2023)
3-139518416-C-T			Uncertain significance (Jan 26, 2024)
3-139518422-A-G		not specified	Uncertain significance (Jan 20, 2024)
3-139518424-G-C			Uncertain significance (Feb 27, 2022)
3-139518430-C-T			Likely benign (Nov 28, 2022)
3-139518431-T-C		not specified	Uncertain significance (Sep 19, 2023)
3-139518437-C-A			Uncertain significance (Oct 27, 2022)
3-139518442-G-A			Likely benign (Dec 11, 2023)
3-139518450-G-A			Uncertain significance (Sep 09, 2023)
3-139518451-G-A			Likely benign (Oct 10, 2022)
3-139518459-C-T			Uncertain significance (Jul 19, 2022)
3-139518460-A-G			Likely benign (May 08, 2023)
3-139518461-C-T		not specified	Uncertain significance (Dec 23, 2023)
3-139518468-CCTT-C			Uncertain significance (Jan 20, 2022)
3-139518470-T-G			Uncertain significance (Nov 30, 2022)
3-139518496-C-A			Uncertain significance (Dec 11, 2023)
3-139518501-C-G			Uncertain significance (Dec 18, 2023)
3-139518504-C-A			Uncertain significance (Dec 27, 2023)
3-139518505-G-A			Benign (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBP1	protein_coding	protein_coding	ENST00000232219	4	22396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000592	0.273	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.625	92	110	0.833	0.00000583	1298
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000579	0.000547
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000463	0.000396
Middle Eastern	0.000489	0.000489
South Asian	0.0000996	0.0000980
Other	0.000542	0.000489

dbNSFP

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}.
• Pathway: Retinoblastoma (RB) in Cancer;Vitamin A and Carotenoid Metabolism;Signaling by GPCR;Signal Transduction;Metabolism of fat-soluble vitamins;Metabolism;The canonical retinoid cycle in rods (twilight vision);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;Retinoic acid receptors-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.322

Intolerance Scores

• loftool: 0.858
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.231
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.525

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbp1
• Phenotype: liver/biliary system phenotype; hematopoietic system phenotype; reproductive system phenotype; pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: retinoid metabolic process;retinoic acid biosynthetic process;vitamin A metabolic process;lipid homeostasis
• Cellular component: nucleoplasm;lipid droplet;cytosol
• Molecular function: retinoid binding;retinal binding;all-trans-retinol binding