RENBP

renin binding protein

Basic information

Region (hg38): X:153935269-153944687

Links

ENSG00000102032 ∙ NCBI:5973 ∙ OMIM:312420 ∙ HGNC:9959 ∙ Uniprot:P51606 ∙ 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 RENBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RENBP 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				2		2
missense			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	15	2	2

Variants in RENBP

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

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

Position	Type	Phenotype	Significance	ClinVar
X-153935300-G-C		not specified	Uncertain significance (Aug 12, 2024)
X-153935307-G-A			Likely benign (Aug 01, 2022)
X-153935333-G-A		not specified	Uncertain significance (Feb 07, 2023)
X-153935374-A-G		not specified	Uncertain significance (Jun 23, 2021)
X-153935408-C-T			Benign (Oct 05, 2017)
X-153935586-C-A			Benign (Mar 02, 2018)
X-153940107-G-A		not specified	Uncertain significance (Aug 11, 2024)
X-153941549-G-A		not specified	Uncertain significance (Apr 20, 2024)
X-153941620-C-T		not specified	Uncertain significance (Sep 06, 2022)
X-153942025-C-T		not specified	Uncertain significance (Feb 17, 2024)
X-153942913-G-A			Benign (Dec 11, 2017)
X-153942977-T-C		not specified	Uncertain significance (Nov 13, 2024)
X-153942985-G-C		not specified	Uncertain significance (Oct 22, 2021)
X-153943012-C-T		not specified	Uncertain significance (Jan 06, 2023)
X-153943028-C-T		not specified	Uncertain significance (Apr 05, 2023)
X-153943072-G-A		not specified	Uncertain significance (Dec 07, 2021)
X-153943073-C-T		not specified	Uncertain significance (Mar 18, 2024)
X-153943078-G-A		not specified	Uncertain significance (Oct 27, 2022)
X-153943637-G-A		not specified	Uncertain significance (Jul 09, 2024)
X-153943683-G-T		not specified	Uncertain significance (Jul 26, 2023)
X-153943704-G-A			Likely benign (Mar 01, 2020)
X-153943898-C-A		not specified	Uncertain significance (Dec 21, 2023)
X-153943938-G-C		not specified	Likely benign (Jun 17, 2024)
X-153944124-G-A		not specified	Uncertain significance (Oct 17, 2024)
X-153944349-C-T		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RENBP	protein_coding	protein_coding	ENST00000393700	11	9517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.449	0.551	125425	3	2	125430	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.791	160	191	0.839	0.0000167	2754
Missense in Polyphen		36	67.571	0.53277		1064
Synonymous	-0.910	87	76.8	1.13	0.00000674	833
Loss of Function	3.14	4	18.6	0.215	0.00000133	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000367	0.0000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000290	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.0000554	0.0000327
Other	0.000224	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the interconversion of N-acetylglucosamine to N-acetylmannosamine. Binds to renin forming a protein complex called high molecular weight (HMW) renin and inhibits renin activity. Involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway: although human is not able to catalyze formation of Neu5Gc due to the inactive CMAHP enzyme, Neu5Gc is present in food and must be degraded. {ECO:0000269|PubMed:9990133}.
• Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Sialuria or French Type Sialuria;Sialuria or French Type Sialuria;Amino Sugar Metabolism;G(M2)-Gangliosidosis: Variant B, Tay-sachs disease;Tay-Sachs Disease;Salla Disease/Infantile Sialic Acid Storage Disease;Aminosugars metabolism;Post-translational protein modification;Metabolism of proteins;Synthesis of UDP-N-acetyl-glucosamine;Synthesis of substrates in N-glycan biosythesis;Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein;Asparagine N-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• rvis_EVS: 1
• rvis_percentile_EVS: 90.62

Haploinsufficiency Scores

• pHI: 0.0875
• hipred: Y
• hipred_score: 0.531
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Renbp
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: N-acetylglucosamine metabolic process;UDP-N-acetylglucosamine biosynthetic process;N-acetylmannosamine metabolic process;regulation of blood pressure;negative regulation of endopeptidase activity;N-acetylneuraminate catabolic process
• Cellular component: cytosol;extracellular exosome
• Molecular function: endopeptidase inhibitor activity;ATP binding;peptidase inhibitor activity;protein homodimerization activity;N-acylglucosamine 2-epimerase activity