NKIRAS1

NFKB inhibitor interacting Ras like 1, the group of RAS type GTPase family

Basic information

Region (hg38): 3:23889951-23946591

Links

ENSG00000197885 ∙ NCBI:28512 ∙ OMIM:604496 ∙ HGNC:17899 ∙ Uniprot:Q9NYS0 ∙ 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 NKIRAS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NKIRAS1 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	14	0	0

Variants in NKIRAS1

This is a list of pathogenic ClinVar variants found in the NKIRAS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-23890535-A-G		not specified	Uncertain significance (Sep 09, 2024)
3-23890542-A-G		not specified	Uncertain significance (Oct 13, 2021)
3-23893163-G-A		not specified	Uncertain significance (Jul 10, 2024)
3-23893169-A-C		not specified	Uncertain significance (Oct 22, 2024)
3-23893219-G-C		not specified	Uncertain significance (Nov 15, 2024)
3-23893297-T-C		not specified	Uncertain significance (Oct 04, 2024)
3-23893331-T-A		not specified	Uncertain significance (Jun 23, 2023)
3-23900831-C-T		not specified	Uncertain significance (Jan 29, 2024)
3-23900906-C-T		not specified	Uncertain significance (Jan 30, 2024)
3-23900972-G-A		not specified	Uncertain significance (Aug 21, 2024)
3-23901014-T-C		not specified	Uncertain significance (Aug 31, 2022)
3-23901022-T-C		not specified	Uncertain significance (Jan 10, 2023)
3-23901035-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-23910849-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-23917732-A-C			Likely benign (Dec 21, 2018)
3-23917766-T-C			Likely benign (Aug 09, 2018)
3-23917859-G-C		not specified	Uncertain significance (Jan 03, 2019)
3-23917877-C-T		RPL15-related disorder	Likely benign (Sep 20, 2023)
3-23917882-A-C			Uncertain significance (May 18, 2023)
3-23917888-T-C		Diamond-Blackfan anemia 12	Pathogenic (May 18, 2023)
3-23917904-G-A			Likely benign (Jun 06, 2023)
3-23917906-C-G			Uncertain significance (Sep 19, 2022)
3-23917907-T-A			Likely benign (Jul 26, 2023)
3-23917914-A-G			Uncertain significance (Jul 19, 2022)
3-23917934-C-G		not specified • RPL15-related disorder	Benign/Likely benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NKIRAS1	protein_coding	protein_coding	ENST00000443659	3	54932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000501	0.699	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.879	74	98.5	0.751	0.00000485	1252
Missense in Polyphen		20	32.151	0.62206		400
Synonymous	0.132	36	37.0	0.972	0.00000196	359
Loss of Function	0.833	6	8.64	0.694	4.48e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000207
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical Ras-like protein that acts as a potent regulator of NF-kappa-B activity by preventing the degradation of NF-kappa-B inhibitor beta (NFKBIB) by most signals, explaining why NFKBIB is more resistant to degradation. May act by blocking phosphorylation of NFKBIB and mediating cytoplasmic retention of p65/RELA NF-kappa-B subunit. It is unclear whether it acts as a GTPase. Both GTP- and GDP-bound forms block phosphorylation of NFKBIB. {ECO:0000269|PubMed:10657303, ECO:0000269|PubMed:12672800, ECO:0000269|PubMed:15024091}.
• Pathway: Toll Like Receptor 7/8 (TLR7/8) Cascade;Signaling by Interleukins;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;ZBP1(DAI) mediated induction of type I IFNs;Toll-Like Receptors Cascades;TRAF6 mediated NF-kB activation;DDX58/IFIH1-mediated induction of interferon-alpha/beta;Interleukin-1 signaling;Innate Immune System;Immune System;RIP-mediated NFkB activation via ZBP1;TAK1 activates NFkB by phosphorylation and activation of IKKs complex;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;TNFalpha;Cytosolic sensors of pathogen-associated DNA ;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Interleukin-1 family signaling (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.724
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.121
• hipred: Y
• hipred_score: 0.796
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nkiras1

Gene ontology

• Biological process: I-kappaB kinase/NF-kappaB signaling
• Cellular component: cellular_component;cytoplasm;membrane
• Molecular function: GTPase activity;GTP binding