RBKS

ribokinase

Basic information

Region (hg38): 2:27781379-27890681

Links

ENSG00000171174 ∙ NCBI:64080 ∙ OMIM:611132 ∙ HGNC:30325 ∙ Uniprot:Q9H477 ∙ 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 RBKS gene.

Variants pathogenicity by type

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

Variants in RBKS

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

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

Position	Type	Phenotype	Significance	ClinVar
2-27781660-C-G		not specified	Uncertain significance (Oct 29, 2021)
2-27781739-T-G		not specified	Uncertain significance (Oct 05, 2023)
2-27781763-G-A		not specified	Uncertain significance (Aug 16, 2021)
2-27827722-C-T		not specified	Uncertain significance (Jul 19, 2022)
2-27832762-T-C		not specified	Uncertain significance (Apr 18, 2023)
2-27843079-G-A		not specified	Uncertain significance (Mar 14, 2023)
2-27843169-C-A		not specified	Uncertain significance (Nov 17, 2022)
2-27847050-T-C		not specified	Uncertain significance (May 03, 2023)
2-27847060-T-C		not specified	Uncertain significance (Oct 26, 2021)
2-27847066-C-A		not specified	Uncertain significance (Jun 22, 2023)
2-27848037-T-G		not specified	Uncertain significance (Jan 19, 2024)
2-27848069-T-G		not specified	Uncertain significance (Feb 23, 2023)
2-27848078-C-T		not specified	Uncertain significance (Apr 10, 2023)
2-27858560-C-T		not specified	Uncertain significance (May 30, 2023)
2-27858561-G-A		not specified	Uncertain significance (Dec 20, 2021)
2-27858572-C-G			Likely benign (Jul 01, 2024)
2-27890333-C-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RBKS	protein_coding	protein_coding	ENST00000302188	8	109735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.16e-9	0.123	123635	17	2096	125748	0.00844

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.252	161	170	0.946	0.00000816	2071
Missense in Polyphen		58	63.176	0.91807		755
Synonymous	0.811	56	64.3	0.871	0.00000326	649
Loss of Function	0.114	13	13.5	0.966	5.65e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00396	0.00395
Ashkenazi Jewish	0.00965	0.00937
East Asian	0.0148	0.0138
Finnish	0.00850	0.00826
European (Non-Finnish)	0.0107	0.0104
Middle Eastern	0.0148	0.0138
South Asian	0.00894	0.00883
Other	0.00879	0.00834

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway. {ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|PubMed:17585908}.
• Pathway: Pentose phosphate pathway - Homo sapiens (human);Pentose Phosphate Pathway;Glucose-6-phosphate dehydrogenase deficiency;Ribose-5-phosphate isomerase deficiency;Transaldolase deficiency;Pentose phosphate pathway (hexose monophosphate shunt);Metabolism of carbohydrates;Metabolism;Pentose phosphate cycle (Consensus)

Intolerance Scores

• loftool: 0.824
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.310
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.528

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rbks

Gene ontology

• Biological process: pentose-phosphate shunt;D-ribose catabolic process;carbohydrate phosphorylation
• Cellular component: nucleus;cytosol
• Molecular function: ribokinase activity;protein binding;ATP binding;metal ion binding