IVNS1ABP

influenza virus NS1A binding protein, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): 1:185296387-185317273

Links

ENSG00000116679 ∙ NCBI:10625 ∙ OMIM:609209 ∙ HGNC:16951 ∙ Uniprot:Q9Y6Y0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency 70 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 70	AD	Allergy/Immunology/Infectious	Individuals may be at increased risk of recurrent infections, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious	32499645

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IVNS1ABP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IVNS1ABP 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				3		3
missense			17	1		18
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	18	4	0

Variants in IVNS1ABP

This is a list of pathogenic ClinVar variants found in the IVNS1ABP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-185298053-TG-T		Immunodeficiency 70	Uncertain significance (Jun 21, 2023)
1-185298054-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-185298065-C-T		Immunodeficiency 70	Pathogenic (Jul 31, 2020)
1-185299710-C-G		IVNS1ABP-related disorder	Uncertain significance (Sep 25, 2023)
1-185300010-G-A		not specified	Uncertain significance (Mar 01, 2024)
1-185300077-C-T		not specified	Uncertain significance (Feb 27, 2024)
1-185300101-T-C		IVNS1ABP-related disorder	Uncertain significance (Jul 12, 2023)
1-185300229-G-A			Uncertain significance (Jan 01, 2022)
1-185300262-C-A		not specified	Uncertain significance (May 26, 2022)
1-185300293-A-G			Likely benign (Jan 01, 2023)
1-185300308-G-C		not specified	Uncertain significance (Oct 26, 2022)
1-185301020-G-A		Immunodeficiency 70	Pathogenic (Jul 31, 2020)
1-185301158-A-G		IVNS1ABP-related disorder	Uncertain significance (Jan 05, 2024)
1-185301203-G-A			Benign (Jul 10, 2018)
1-185301455-C-T			Likely benign (Nov 01, 2022)
1-185307017-T-A		not specified	Uncertain significance (Dec 20, 2023)
1-185307061-G-A		Immunodeficiency 70 • not specified	Uncertain significance (Mar 25, 2024)
1-185307066-A-C		not specified	Uncertain significance (Oct 03, 2022)
1-185307118-T-G		not specified	Uncertain significance (Jul 12, 2023)
1-185307516-C-G		not specified	Uncertain significance (Jun 03, 2024)
1-185307641-A-G		IVNS1ABP-related disorder	Uncertain significance (Jan 24, 2023)
1-185308881-T-TA		IVNS1ABP-related disorder	Likely benign (Oct 18, 2023)
1-185308882-A-T		IVNS1ABP-related disorder	Likely benign (Jan 05, 2024)
1-185309044-T-C		IVNS1ABP-related disorder	Likely benign (Apr 11, 2023)
1-185309048-T-C		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IVNS1ABP	protein_coding	protein_coding	ENST00000367498	13	20942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00558	125728	0	10	125738	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	192	342	0.561	0.0000168	4255
Missense in Polyphen		30	90.152	0.33277		1067
Synonymous	1.93	92	119	0.775	0.00000585	1174
Loss of Function	4.91	5	37.5	0.133	0.00000235	416

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000580	0.0000580
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000615
Middle Eastern	0.0000547	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in many cell functions, including pre-mRNA splicing, the aryl hydrocarbon receptor (AHR) pathway, F-actin organization and protein ubiquitination. Plays a role in the dynamic organization of the actin skeleton as a stabilizer of actin filaments by association with F-actin through Kelch repeats (By similarity). Protects cells from cell death induced by actin destabilization (By similarity). Functions as modifier of the AHR/Aryl hydrocarbon receptor pathway increasing the concentration of AHR available to activate transcription (PubMed:16582008). In addition, functions as a negative regulator of BCR(KLHL20) E3 ubiquitin ligase complex to prevent ubiquitin-mediated proteolysis of PML and DAPK1, two tumor suppressors (PubMed:25619834). Inhibits pre-mRNA splicing (in vitro) (PubMed:9696811). {ECO:0000250|UniProtKB:Q920Q8, ECO:0000269|PubMed:16582008, ECO:0000269|PubMed:25619834, ECO:0000269|PubMed:9696811}.
• Pathway: Influenza A - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.299
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.279
• hipred: Y
• hipred_score: 0.728
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ivns1abp
• 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); respiratory system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype

Gene ontology

• Biological process: transcription by RNA polymerase III;RNA splicing;response to virus;viral process;negative regulation of protein ubiquitination;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleoplasm;transcription factor complex;spliceosomal complex;cytosol;actin cytoskeleton
• Molecular function: protein binding