RPS19BP1

ribosomal protein S19 binding protein 1

Basic information

Region (hg38): 22:39529093-39532761

Links

ENSG00000187051 ∙ NCBI:91582 ∙ OMIM:610225 ∙ HGNC:28749 ∙ Uniprot:Q86WX3 ∙ 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 RPS19BP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS19BP1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in RPS19BP1

This is a list of pathogenic ClinVar variants found in the RPS19BP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-39529586-C-T		not specified	Uncertain significance (Dec 15, 2022)
22-39529902-C-T		not specified	Uncertain significance (Oct 30, 2024)
22-39529908-C-T		not specified	Likely benign (Jul 22, 2024)
22-39532412-A-G		not specified	Uncertain significance (Jan 29, 2025)
22-39532446-C-G		not specified	Uncertain significance (Feb 27, 2024)
22-39532511-G-A		not specified	Uncertain significance (Aug 10, 2024)
22-39532705-G-C		not specified	Uncertain significance (Aug 02, 2024)
22-39532713-C-G		not specified	Uncertain significance (Jan 01, 2025)
22-39532713-C-T		not specified	Uncertain significance (May 04, 2023)
22-39532726-G-C		not specified	Uncertain significance (Jan 21, 2025)
22-39532729-C-A		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS19BP1	protein_coding	protein_coding	ENST00000334678	4	3763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000267	0.333	125718	0	27	125745	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.401	74	84.4	0.877	0.00000478	849
Missense in Polyphen		17	28.065	0.60573		310
Synonymous	0.420	32	35.2	0.910	0.00000173	289
Loss of Function	0.0715	7	7.21	0.971	4.54e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Direct regulator of SIRT1. Enhances SIRT1-mediated deacetylation of p53/TP53, thereby participating in inhibition of p53/TP53-mediated transcriptional activity. {ECO:0000269|PubMed:17964266}.
• Pathway: Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: 0.21
• rvis_percentile_EVS: 67.72

Haploinsufficiency Scores

• pHI: 0.126
• hipred: Y
• hipred_score: 0.506
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.398

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps19bp1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol
• Molecular function: RNA binding;protein binding;enzyme binding