NKRF

NFKB repressing factor, the group of G-patch domain containing

Basic information

Region (hg38): X:119588337-119606443

Links

ENSG00000186416 ∙ NCBI:55922 ∙ OMIM:300440 ∙ HGNC:19374 ∙ Uniprot:O15226 ∙ 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 NKRF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKRF 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	3	5
missense			27	1		28
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2		2
Total	0	0	27	5	4

Variants in NKRF

This is a list of pathogenic ClinVar variants found in the NKRF 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-119589405-T-C		not specified	Uncertain significance (Nov 09, 2024)
X-119589444-C-T		not specified	Uncertain significance (May 20, 2024)
X-119589490-A-G			Benign (Apr 16, 2018)
X-119589548-C-G		not specified	Likely benign (Feb 19, 2025)
X-119589581-C-T		not specified	Uncertain significance (Aug 11, 2024)
X-119589771-C-T		not specified	Uncertain significance (Jan 17, 2024)
X-119589783-G-T		not specified	Uncertain significance (Jan 04, 2024)
X-119589972-C-G		not specified	Uncertain significance (Oct 01, 2024)
X-119589998-A-C		not specified	Uncertain significance (Feb 05, 2024)
X-119589999-G-A		not specified	Uncertain significance (Feb 27, 2024)
X-119590008-T-A		not specified	Uncertain significance (Dec 17, 2024)
X-119590139-G-A		not specified	Uncertain significance (Apr 13, 2022)
X-119590170-C-T		not specified	Uncertain significance (Feb 12, 2025)
X-119590186-C-A		not specified	Uncertain significance (May 08, 2024)
X-119590377-T-C		not specified	Uncertain significance (Nov 14, 2023)
X-119590431-C-T		not specified	Uncertain significance (May 04, 2023)
X-119590448-C-A		not specified	Uncertain significance (Oct 20, 2024)
X-119590449-C-T		not specified	Uncertain significance (Mar 06, 2025)
X-119590450-G-A			Benign (Jan 09, 2018)
X-119590463-C-A		not specified	Uncertain significance (May 14, 2024)
X-119590542-G-C		not specified	Uncertain significance (Jan 16, 2024)
X-119590575-G-A		not specified	Uncertain significance (May 04, 2022)
X-119590596-G-A		not specified	Uncertain significance (Nov 14, 2024)
X-119590716-T-C		not specified	Uncertain significance (Dec 21, 2022)
X-119590812-G-A		not specified	Uncertain significance (Sep 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKRF	protein_coding	protein_coding	ENST00000542113	3	17559

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00339	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	145	272	0.533	0.0000210	4628
Missense in Polyphen		27	88.456	0.30524		1528
Synonymous	1.21	83	98.2	0.845	0.00000755	1364
Loss of Function	3.79	0	16.7	0.00	0.00000124	332

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with a specific negative regulatory element (NRE) 5'-AATTCCTCTGA-3' to mediate transcriptional repression of certain NK-kappa-B responsive genes. Involved in the constitutive silencing of the interferon beta promoter, independently of the virus-induced signals, and in the inhibition of the basal and cytokine-induced iNOS promoter activity. Also involved in the regulation of IL-8 transcription. {ECO:0000269|PubMed:12381793}.

Recessive Scores

• pRec: 0.210

Intolerance Scores

• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.486
• hipred: Y
• hipred_score: 0.590
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkrf
• Phenotype: normal phenotype

Gene ontology

• Biological process: negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;RNA binding;protein binding