TRAF5

TNF receptor associated factor 5, the group of Zinc fingers TRAF-type|TNF receptor associated factors|Ring finger proteins

Basic information

Region (hg38): 1:211326614-211374946

Links

ENSG00000082512 ∙ NCBI:7188 ∙ OMIM:602356 ∙ HGNC:12035 ∙ Uniprot:O00463 ∙ 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 TRAF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAF5 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in TRAF5

This is a list of pathogenic ClinVar variants found in the TRAF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-211353273-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-211353283-T-A		not specified	Uncertain significance (Jul 06, 2022)
1-211353285-C-T		not specified	Uncertain significance (Apr 04, 2023)
1-211353286-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-211353426-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-211353427-G-A		not specified	Uncertain significance (Jun 01, 2023)
1-211353451-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-211354411-G-A		not specified	Uncertain significance (Jan 31, 2022)
1-211354421-C-G		not specified	Uncertain significance (Feb 14, 2024)
1-211354439-T-C		not specified	Uncertain significance (Jan 30, 2024)
1-211356383-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-211356409-T-C		not specified	Uncertain significance (Aug 24, 2023)
1-211356425-A-G		not specified	Uncertain significance (Mar 21, 2023)
1-211359927-T-C		not specified	Uncertain significance (Jan 03, 2024)
1-211359931-T-C		not specified	Uncertain significance (Oct 25, 2022)
1-211360005-A-C		not specified	Uncertain significance (Jun 07, 2023)
1-211360059-G-A		not specified	Uncertain significance (May 18, 2022)
1-211360062-G-A		not specified	Uncertain significance (Jun 04, 2024)
1-211360715-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-211360756-G-T		not specified	Uncertain significance (Feb 12, 2024)
1-211361131-G-A		not specified	Uncertain significance (Dec 05, 2022)
1-211365382-C-T		not specified	Uncertain significance (May 29, 2024)
1-211365431-G-A		not specified	Uncertain significance (Mar 20, 2024)
1-211369465-A-T		not specified	Uncertain significance (Dec 06, 2021)
1-211369548-G-A		not specified	Uncertain significance (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAF5	protein_coding	protein_coding	ENST00000261464	10	48332

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.67e-12	0.350	125661	1	86	125748	0.000346

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.960	252	299	0.844	0.0000159	3707
Missense in Polyphen		82	111.92	0.73269		1298
Synonymous	1.07	96	110	0.871	0.00000534	987
Loss of Function	1.18	22	28.9	0.762	0.00000146	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000756	0.000739
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000329	0.000308
Middle Eastern	0.000435	0.000435
South Asian	0.000832	0.000784
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter protein and signal transducer that links members of the tumor necrosis factor receptor family to different signaling pathways by association with the receptor cytoplasmic domain and kinases. Mediates activation of NF-kappa-B and probably JNK. Seems to be involved in apoptosis. Plays a role in mediating activation of NF-kappa-B by EIF2AK2/PKR. {ECO:0000269|PubMed:15121867}.
• Pathway: Small cell lung cancer - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Necroptosis - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);RANKL-RANK (Receptor activator of NFKB (ligand)) Signaling Pathway;TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway;Photodynamic therapy-induced AP-1 survival signaling.;TWEAK;yaci and bcma stimulation of b cell immune responses;TNFalpha;RANKL (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.957
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.0840
• hipred: Y
• hipred_score: 0.715
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Traf5
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;signal transduction;regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of DNA-binding transcription factor activity;positive regulation of NF-kappaB transcription factor activity
• Cellular component: centrosome;cytosol;cytoplasmic side of plasma membrane;protein-containing complex;CD40 receptor complex
• Molecular function: tumor necrosis factor receptor binding;protein binding;zinc ion binding;ubiquitin protein ligase binding;thioesterase binding;identical protein binding