RBP5

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

Basic information

Region (hg38): 12:7115735-7128889

Links

ENSG00000139194 ∙ NCBI:83758 ∙ OMIM:611866 ∙ HGNC:15847 ∙ Uniprot:P82980 ∙ 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 RBP5 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RBP5 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 RBP5

This is a list of pathogenic ClinVar variants found in the RBP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7124667-C-T		not specified	Uncertain significance (Oct 10, 2023)
12-7124720-G-A		not specified	Uncertain significance (Mar 07, 2024)
12-7128260-C-A		not specified	Uncertain significance (May 18, 2023)
12-7128277-T-C		not specified	Uncertain significance (Jul 21, 2021)
12-7128301-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-7128328-A-G		not specified	Uncertain significance (Sep 06, 2022)
12-7128343-A-T		not specified	Uncertain significance (Nov 30, 2022)
12-7128346-T-G		not specified	Uncertain significance (Sep 06, 2022)
12-7128367-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-7128374-C-T		not specified	Uncertain significance (Dec 21, 2021)
12-7128380-T-G		not specified	Uncertain significance (Jul 11, 2022)
12-7128404-C-T		not specified	Uncertain significance (May 25, 2022)
12-7128726-A-G		not specified	Uncertain significance (Sep 17, 2021)
12-7128748-G-A		not specified	Likely benign (Aug 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBP5	protein_coding	protein_coding	ENST00000266560	4	5259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000492	0.442	125698	0	49	125747	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.402	70	80.1	0.874	0.00000481	866
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000437	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000437	0.000435
South Asian	0.000427	0.000425
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Intracellular transport of retinol. {ECO:0000269|PubMed:11274389}.
• Pathway: retinoate biosynthesis II;retinoate biosynthesis I;retinol biosynthesis;the visual cycle I (vertebrates) (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.676
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.42

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.310

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.460

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm;extracellular exosome
• Molecular function: retinoid binding;protein binding;retinal binding;retinol binding