TRAF3IP3

TRAF3 interacting protein 3

Basic information

Region (hg38): 1:209756032-209782320

Links

ENSG00000009790 ∙ NCBI:80342 ∙ OMIM:608255 ∙ HGNC:30766 ∙ Uniprot:Q9Y228 ∙ 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 TRAF3IP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAF3IP3 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in TRAF3IP3

This is a list of pathogenic ClinVar variants found in the TRAF3IP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-209760047-G-T		not specified	Uncertain significance (Oct 26, 2022)
1-209760055-C-T		not specified	Uncertain significance (Sep 28, 2022)
1-209760056-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-209760067-C-T		not specified	Uncertain significance (May 09, 2023)
1-209760080-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-209760146-G-A		not specified	Uncertain significance (Oct 14, 2021)
1-209760152-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-209760167-G-A		not specified	Uncertain significance (Dec 13, 2022)
1-209760167-G-T		not specified	Uncertain significance (Dec 15, 2022)
1-209760182-C-T		not specified	Uncertain significance (May 20, 2024)
1-209760275-C-T		not specified	Uncertain significance (Feb 15, 2023)
1-209760289-G-A		not specified	Uncertain significance (Sep 20, 2023)
1-209760304-C-A		not specified	Uncertain significance (Mar 28, 2023)
1-209762531-C-A		not specified	Uncertain significance (May 30, 2024)
1-209762570-T-C		not specified	Uncertain significance (Apr 19, 2024)
1-209762584-T-G		not specified	Likely benign (Jun 07, 2023)
1-209762660-G-T		not specified	Uncertain significance (Jun 22, 2024)
1-209762826-G-C		not specified	Uncertain significance (Feb 16, 2023)
1-209772974-G-C		not specified	Uncertain significance (Feb 01, 2023)
1-209772988-C-G		not specified	Uncertain significance (Mar 20, 2023)
1-209775356-C-T		not specified	Uncertain significance (May 21, 2024)
1-209775600-G-A		not specified	Uncertain significance (May 05, 2023)
1-209775703-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-209777359-A-G		not specified	Uncertain significance (Oct 02, 2023)
1-209777484-C-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAF3IP3	protein_coding	protein_coding	ENST00000367024	15	26292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-12	0.958	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.714	251	285	0.881	0.0000148	3586
Missense in Polyphen		61	69.04	0.88355		914
Synonymous	1.57	90	111	0.810	0.00000546	1030
Loss of Function	2.21	25	40.1	0.623	0.00000210	422

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000420	0.000420
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000247	0.000246
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as an adapter molecule that regulates TRAF3-mediated JNK activation. {ECO:0000250}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.786
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.5

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.273
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.678

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Traf3ip3
• Phenotype: endocrine/exocrine gland phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding