RFK

riboflavin kinase

Basic information

Region (hg38): 9:76385526-76394517

Links

ENSG00000135002 ∙ NCBI:55312 ∙ OMIM:613010 ∙ HGNC:30324 ∙ Uniprot:Q969G6 ∙ 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 RFK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RFK 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in RFK

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

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

Position	Type	Phenotype	Significance	ClinVar
9-76387404-G-A		not specified	Uncertain significance (Jul 06, 2021)
9-76387479-G-T		not specified	Uncertain significance (Oct 05, 2022)
9-76387506-C-T		not specified	Uncertain significance (Nov 18, 2022)
9-76388637-G-C		not specified	Uncertain significance (Jul 14, 2021)
9-76388639-A-T		not specified	Uncertain significance (Jul 14, 2021)
9-76392420-T-C		not specified	Uncertain significance (Mar 15, 2024)
9-76392492-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-76392495-C-T		not specified	Uncertain significance (May 14, 2024)
9-76392524-G-A		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RFK	protein_coding	protein_coding	ENST00000376736	4	9001

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0639	0.877	125741	0	5	125746	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.493	69	81.5	0.846	0.00000364	1021
Missense in Polyphen		16	22.968	0.69661		315
Synonymous	-0.533	32	28.4	1.13	0.00000129	280
Loss of Function	1.59	3	7.78	0.386	4.26e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000114	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the phosphorylation of riboflavin (vitamin B2) to form flavin-mononucleotide (FMN), hence rate-limiting enzyme in the synthesis of FAD. Essential for TNF-induced reactive oxygen species (ROS) production. Through its interaction with both TNFRSF1A and CYBA, physically and functionally couples TNFRSF1A to NADPH oxidase. TNF-activation of RFK may enhance the incorporation of FAD in NADPH oxidase, a critical step for the assembly and activation of NADPH oxidase. {ECO:0000269|PubMed:19641494}.
• Pathway: Riboflavin metabolism - Homo sapiens (human);Riboflavin Metabolism;Selenium Micronutrient Network;Folate Metabolism;TNF alpha Signaling Pathway;Metabolism;Vitamin B2 (riboflavin) metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors;flavin biosynthesis;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.182
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.0665
• hipred: N
• hipred_score: 0.332
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.396

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rfk
• Phenotype: homeostasis/metabolism 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); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: riboflavin metabolic process;apoptotic process;riboflavin biosynthetic process;FMN biosynthetic process;phosphorylation;positive regulation of NAD(P)H oxidase activity;reactive oxygen species metabolic process
• Cellular component: cytoplasm;cytosol
• Molecular function: protein binding;ATP binding;riboflavin kinase activity;metal ion binding