NFRKB

nuclear factor related to kappaB binding protein, the group of INO80 complex

Basic information

Region (hg38): 11:129863636-129895590

Links

ENSG00000170322 ∙ NCBI:4798 ∙ OMIM:164013 ∙ HGNC:7802 ∙ Uniprot:Q6P4R8 ∙ 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 NFRKB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFRKB 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			91	3		94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	91	5	0

Variants in NFRKB

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

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

Position	Type	Phenotype	Significance	ClinVar
11-129864738-G-A		not specified	Uncertain significance (Jul 26, 2024)
11-129864801-G-C		not specified	Uncertain significance (Nov 03, 2023)
11-129864846-C-T		not specified	Uncertain significance (Sep 20, 2023)
11-129865079-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-129865887-G-A		not specified	Uncertain significance (Jun 17, 2022)
11-129865889-T-C		not specified	Uncertain significance (Mar 06, 2023)
11-129865932-T-A		not specified	Uncertain significance (Dec 02, 2022)
11-129869504-G-A		not specified	Uncertain significance (Nov 21, 2024)
11-129869541-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-129869546-G-C		not specified	Uncertain significance (May 13, 2024)
11-129869550-C-A		not specified	Uncertain significance (Dec 28, 2023)
11-129869583-C-G		not specified	Uncertain significance (Oct 08, 2024)
11-129869642-G-A		not specified	Uncertain significance (Oct 21, 2024)
11-129869657-G-T		not specified	Uncertain significance (Aug 17, 2022)
11-129869677-C-T		not specified	Likely benign (Jun 01, 2023)
11-129869678-G-A		not specified	Uncertain significance (Dec 10, 2024)
11-129869715-T-C		not specified	Uncertain significance (Apr 13, 2022)
11-129869804-T-C		not specified	Uncertain significance (Dec 14, 2024)
11-129869808-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-129869856-C-T		not specified	Uncertain significance (Nov 30, 2021)
11-129869888-G-A		not specified	Uncertain significance (Feb 07, 2025)
11-129869930-G-A		not specified	Uncertain significance (Nov 09, 2023)
11-129869992-G-C		not specified	Uncertain significance (Oct 16, 2023)
11-129870079-C-G		not specified	Uncertain significance (Nov 26, 2024)
11-129870099-T-C		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFRKB	protein_coding	protein_coding	ENST00000524794	25	31955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.134	0.866	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	659	779	0.845	0.0000473	8518
Missense in Polyphen		172	213.13	0.80701		2318
Synonymous	-1.66	343	306	1.12	0.0000187	2817
Loss of Function	5.58	15	62.7	0.239	0.00000330	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000462	0.000391
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000186	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'. {ECO:0000269|PubMed:18922472}.
• Pathway: Overview of nanoparticle effects;DNA Repair;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination;DNA Damage Recognition in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.0267
• rvis_EVS: -2.65
• rvis_percentile_EVS: 0.76

Haploinsufficiency Scores

• pHI: 0.213
• hipred: Y
• hipred_score: 0.747
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.632

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfrkb

Gene ontology

• Biological process: DNA repair;DNA recombination;transcription by RNA polymerase II;inflammatory response;protein deubiquitination
• Cellular component: nucleus;nucleoplasm;Ino80 complex
• Molecular function: protease binding;DNA binding;protein binding