TRAF1

TNF receptor associated factor 1, the group of TNF receptor associated factors

Basic information

Region (hg38): 9:120902392-120929173

Links

ENSG00000056558 ∙ NCBI:7185 ∙ OMIM:601711 ∙ HGNC:12031 ∙ Uniprot:Q13077 ∙ 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 TRAF1 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAF1 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				1	2	3
missense			10	2		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	2

Variants in TRAF1

This is a list of pathogenic ClinVar variants found in the TRAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-120905165-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-120905184-G-A		not specified	Uncertain significance (Dec 02, 2021)
9-120905208-G-A		not specified	Uncertain significance (Jun 13, 2022)
9-120909242-G-A		not specified	Benign (Mar 28, 2016)
9-120909335-C-T			Benign (Jul 04, 2018)
9-120911354-C-T		not specified	Likely benign (Aug 16, 2021)
9-120911457-C-A		not specified	Uncertain significance (Feb 02, 2022)
9-120913356-C-T		not specified	Uncertain significance (Aug 13, 2021)
9-120913536-C-T		not specified	Uncertain significance (Jan 03, 2024)
9-120913574-G-A			Likely benign (May 03, 2018)
9-120913647-C-T		not specified	Likely benign (Nov 18, 2022)
9-120913669-A-G		not specified	Uncertain significance (Oct 03, 2022)
9-120913681-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-120914242-G-C		not specified	Uncertain significance (Jun 11, 2021)
9-120914248-C-T		not specified	Uncertain significance (Dec 12, 2023)
9-120914254-C-T		not specified	Uncertain significance (Oct 14, 2023)
9-120914291-C-T		not specified	Uncertain significance (Mar 22, 2023)
9-120923718-C-T		not specified	Uncertain significance (Nov 08, 2022)
9-120925941-G-C		not specified	Uncertain significance (Oct 26, 2022)
9-120926000-C-T		not specified	Uncertain significance (Nov 02, 2023)
9-120926048-G-A		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAF1	protein_coding	protein_coding	ENST00000373887	7	26781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00356	0.988	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.920	206	247	0.835	0.0000145	2707
Missense in Polyphen		52	78.935	0.65877		909
Synonymous	1.27	90	107	0.843	0.00000653	835
Loss of Function	2.31	7	17.4	0.403	8.05e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000202	0.000202
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Adapter molecule that regulates the activation of NF- kappa-B and JNK. Plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of a E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein- ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2. {ECO:0000269|PubMed:10692572, ECO:0000269|PubMed:16323247, ECO:0000269|PubMed:18429822, ECO:0000269|PubMed:19287455, ECO:0000269|PubMed:19698991, ECO:0000269|PubMed:20385093}.
• Pathway: Small cell lung cancer - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Apoptosis - 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;TNF alpha Signaling Pathway;Apoptosis;EBV LMP1 signaling;Apoptosis-related network due to altered Notch3 in ovarian cancer;Apoptotic Signaling Pathway;Oxidative Damage;TWEAK;Signal Transduction;tnfr2 signaling pathway;hiv-1 nef: negative effector of fas and tnf;keratinocyte differentiation;TNFR1-induced NFkappaB signaling pathway;TNF signaling;Death Receptor Signalling;Regulation of TNFR1 signaling;TNFalpha;RANKL;HIV-1 Nef: Negative effector of Fas and TNF-alpha;CD40/CD40L signaling;TNF receptor signaling pathway (Consensus)

Recessive Scores

• pRec: 0.395

Intolerance Scores

• loftool: 0.644
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.645
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.869

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Traf1
• Phenotype: cellular phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: apoptotic process;signal transduction;regulation of tumor necrosis factor-mediated signaling pathway;positive regulation of NF-kappaB transcription factor activity;protein-containing complex assembly;regulation of extrinsic apoptotic signaling pathway
• Cellular component: cytoplasm;cytosol;protein-containing complex
• Molecular function: tumor necrosis factor receptor binding;protein binding;zinc ion binding;ubiquitin protein ligase binding;thioesterase binding;identical protein binding