TRAF5

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

Basic information

Region (hg38): 1:211326615-211374946

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.

not_specified (78 variants)
Multiple_myeloma (1 variants)

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. These statistics are base on transcript: NM_001033910.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			76 clinvar	1 clinvar		77
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	76	2	0

Highest pathogenic variant AF is 0.00000371735

Loading clinvar variants...

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