TRAF3IP2

TRAF3 interacting protein 2

Basic information

Region (hg38): 6:111555381-111606906

Previous symbols: [ "C6orf4", "C6orf5", "C6orf6", "C6orf2" ]

Links

ENSG00000056972 ∙ NCBI:10758 ∙ OMIM:607043 ∙ HGNC:1343 ∙ Uniprot:O43734 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• chronic mucocutaneous candidiasis (Supportive), mode of inheritance: AD
• candidiasis, familial, 8 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Candidiasis, familial 8	AR	Allergy/Immunology/Infectious	Individuals have been reported as having recurrent candidal (and other) infections, and surveillance, prophylaxis, and early treatment may be beneficial	Allergy/Immunology/Infectious	24120361

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAF3IP2 gene.

• Candidiasis, familial, 8 (8 variants)
• Discoid lupus erythematosus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAF3IP2 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				54	3	57
missense	1		119	7	7	134
nonsense	4		2			6
start loss						0
frameshift	4		1			5
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)		3				3
splice region			2	7	2	11
non coding			2	15	2	19
Total	9	3	125	76	13

Highest pathogenic variant AF is 0.0000197

Variants in TRAF3IP2

This is a list of pathogenic ClinVar variants found in the TRAF3IP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-111559411-G-C		Candidiasis, familial, 8	Likely benign (Jul 13, 2020)
6-111559417-C-A		Candidiasis, familial, 8	Likely benign (Jun 03, 2023)
6-111559422-G-A		Candidiasis, familial, 8	Uncertain significance (Feb 20, 2018)
6-111559423-A-G		Candidiasis, familial, 8	Likely benign (Apr 18, 2022)
6-111559426-G-C		Candidiasis, familial, 8	Likely benign (Jun 24, 2023)
6-111559429-G-T		Candidiasis, familial, 8	Likely benign (Apr 12, 2023)
6-111559442-C-T		not specified	Uncertain significance (Jan 27, 2022)
6-111559467-C-T		Candidiasis, familial, 8	Uncertain significance (Apr 21, 2022)
6-111559489-G-A		Candidiasis, familial, 8	Benign (Jan 03, 2024)
6-111559489-G-GT		Candidiasis, familial, 8	Uncertain significance (Dec 22, 2023)
6-111559506-G-A		Candidiasis, familial, 8	Uncertain significance (Dec 11, 2023)
6-111559520-T-C		Candidiasis, familial, 8	Benign (Jan 24, 2024)
6-111559523-G-A		Candidiasis, familial, 8	Pathogenic (Oct 17, 2013)
6-111559528-C-T		Candidiasis, familial, 8	Likely benign (Aug 03, 2020)
6-111559529-T-C		Candidiasis, familial, 8	Uncertain significance (Jul 12, 2022)
6-111559535-C-G		Psoriasis 13, susceptibility to	Uncertain significance (Mar 17, 2024)
6-111559539-T-C		Candidiasis, familial, 8	Uncertain significance (Apr 03, 2021)
6-111559551-C-A		Candidiasis, familial, 8	Uncertain significance (Jun 05, 2018)
6-111559557-G-T		Candidiasis, familial, 8	Likely benign (Dec 25, 2023)
6-111562947-GT-G		Candidiasis, familial, 8	Likely benign (Dec 11, 2023)
6-111562947-GTTTC-G		Candidiasis, familial, 8	Likely benign (Jan 22, 2024)
6-111562951-C-G		Candidiasis, familial, 8	Likely benign (May 15, 2023)
6-111562951-CTTTG-C		Candidiasis, familial, 8	Likely benign (Nov 27, 2023)
6-111562986-C-T		Candidiasis, familial, 8	Likely benign (Nov 27, 2023)
6-111562992-G-A		Candidiasis, familial, 8	Likely benign (Jul 30, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAF3IP2	protein_coding	protein_coding	ENST00000368761	8	49825

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.61e-9	0.834	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	235	317	0.742	0.0000167	3671
Missense in Polyphen		55	96.862	0.56782		1178
Synonymous	0.780	116	127	0.912	0.00000740	1143
Loss of Function	1.65	18	27.3	0.660	0.00000161	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000311	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000275	0.000272
Finnish	0.000926	0.000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000275	0.000272
South Asian	0.000174	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could be involved in the activation of both NF-kappa-B via a NF-kappa-B inhibitor kinase (IKK)-dependent mechanism and stress-activated protein kinase (SAPK)/JNK.
• Disease: DISEASE: Candidiasis, familial, 8 (CANDF8) [MIM:615527]: A primary immunodeficiency disorder with altered immune responses and impaired clearance of fungal infections, selective against Candida. It is characterized by persistent and/or recurrent infections of the skin, nails and mucous membranes caused by organisms of the genus Candida, mainly Candida albicans. {ECO:0000269|PubMed:24120361}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: IL-17 signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);IL17 signaling pathway (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.84

Haploinsufficiency Scores

• pHI: 0.0885
• hipred: N
• hipred_score: 0.440
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Traf3ip2
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; digestive/alimentary phenotype; vision/eye phenotype; 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); hematopoietic system phenotype; reproductive system 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)

Gene ontology

• Biological process: B cell apoptotic process;positive regulation of defense response to virus by host;humoral immune response;intracellular signal transduction;positive regulation of I-kappaB kinase/NF-kappaB signaling;immunoglobulin secretion
• Cellular component: cellular_component
• Molecular function: signaling receptor binding;protein binding