TRAIP (TRAF interacting protein)

Gene

• Entrez ID: 10293
• Gene name: TRAF interacting protein
• Gene symbol: TRAIP
• Synonyms (NCBI Gene): RNF206, SCKL9, TRIP
• Chromosome: 3
• Chromosome location: 3p21.31
• Summary: This gene encodes a protein that contains an N-terminal RING finger motif and a putative coiled-coil domain. A similar murine protein interacts with TNFR-associated factor 1 (TRAF1), TNFR-associated factor 2 (TRAF2), and cylindromatosis. The interaction w

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs767664526	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, intron variant, stop gained
rs864622784	G>A	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022218	hsa-miR-124-3p	Microarray	18668037
MIRT024554	hsa-miR-215-5p	Microarray	19074876
MIRT025570	hsa-miR-34a-5p	Proteomics	21566225
MIRT026188	hsa-miR-192-5p	Microarray	19074876
MIRT1451312	hsa-miR-3135	CLIP-seq
MIRT1451313	hsa-miR-3714	CLIP-seq
MIRT1451314	hsa-miR-4736	CLIP-seq
MIRT1451315	hsa-miR-548an	CLIP-seq
MIRT1451316	hsa-miR-940	CLIP-seq
MIRT2134924	hsa-miR-3620	CLIP-seq
MIRT2134925	hsa-miR-3622a-3p	CLIP-seq
MIRT2134926	hsa-miR-3622b-3p	CLIP-seq
MIRT2649653	hsa-miR-1286	CLIP-seq
MIRT2649654	hsa-miR-3660	CLIP-seq
MIRT2649655	hsa-miR-370	CLIP-seq
MIRT2649656	hsa-miR-4526	CLIP-seq
MIRT2649657	hsa-miR-492	CLIP-seq
MIRT2649658	hsa-miR-628-5p	CLIP-seq
MIRT2649653	hsa-miR-1286	CLIP-seq
MIRT2649654	hsa-miR-3660	CLIP-seq
MIRT2649655	hsa-miR-370	CLIP-seq
MIRT2649656	hsa-miR-4526	CLIP-seq
MIRT2649657	hsa-miR-492	CLIP-seq
MIRT2649658	hsa-miR-628-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004842	Function	Ubiquitin-protein transferase activity	IDA	17544371
GO:0004842	Function	Ubiquitin-protein transferase activity	IEA
GO:0005515	Function	Protein binding	IPI	17474147, 25416956, 26711499, 27462463, 31515488, 32296183, 32814053
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA	30165463
GO:0005654	Component	Nucleoplasm	IEA
GO:0005694	Component	Chromosome	IEA
GO:0005730	Component	Nucleolus	IDA	27462463, 30165463
GO:0005730	Component	Nucleolus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006915	Process	Apoptotic process	TAS	9104814
GO:0006974	Process	DNA damage response	IDA	26711499, 27462463
GO:0006974	Process	DNA damage response	IEA
GO:0007165	Process	Signal transduction	IEA
GO:0007165	Process	Signal transduction	IEA
GO:0007165	Process	Signal transduction	TAS	9104814
GO:0008270	Function	Zinc ion binding	IEA
GO:0010804	Process	Negative regulation of tumor necrosis factor-mediated signaling pathway	IDA	19151749
GO:0016567	Process	Protein ubiquitination	IBA
GO:0016567	Process	Protein ubiquitination	IDA	17544371, 26711499
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0031297	Process	Replication fork processing	IBA
GO:0031297	Process	Replication fork processing	IDA	26711499
GO:0031297	Process	Replication fork processing	IMP	27462463
GO:0032688	Process	Negative regulation of interferon-beta production	IEA
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IBA
GO:0061630	Function	Ubiquitin protein ligase activity	IEA
GO:0090734	Component	Site of DNA damage	IBA
GO:0090734	Component	Site of DNA damage	IDA	26711499, 30165463
GO:0106300	Process	Protein-DNA covalent cross-linking repair	ISS

Other IDs

• MIM: 605958
• HGNC: 30764
• e!Ensembl: ENSG00000183763

Protein

• UniProt ID: Q9BWF2
• Protein name: E3 ubiquitin-protein ligase TRAIP (EC 2.3.2.27) (RING finger protein 206) (TRAF-interacting protein)
• Protein function: E3 ubiquitin ligase required to protect genome stability in response to replication stress (PubMed:25335891, PubMed:26595769, PubMed:26711499, PubMed:26781088, PubMed:27462463, PubMed:31545170). Acts as a key regulator of interstrand cross-link
• PDB: 4ZTD
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF13639	zf-RING_2	5 → 50	Ring finger domain	Domain

• Sequence:

  MPIRALCTICSDFFDHSRDVAAIHCGHTFHLQCLIQWFETAPSRTCPQCRIQVGKRTIIN
  KLFFDLAQEEENVLDAEFLKNELDNVRAQLSQKDKEKRDSQVIIDTLRDTLEERNATVVS
  LQQALGKAEMLCSTLKKQMKYLEQQQDETKQAQEEARRLRSKMKTMEQIELLLQSQRPEV
  EEMIRDMGVGQSAVEQLAVYCVSLKKEYENLKEARKASGEVADKLRKDLFSSRSKLQTVY
  SELDQAKLELKSAQKDLQSADKEIMSLKKKLTMLQETLNLPPVASETVDRLVLESPAPVE
  VNLKLRRPSFRDDIDLNATFDVDTPPARPSSSQHGYYEKLCLEKSHSPIQDVPKKICKGP
  RKESQLSLGGQSCAGEPDEELVGAFPIFVRNAILGQKQPKRPRSESSCSKDVVRTGFDGL
  GGRTKFIQPTDTVMIRPLPVKPKTKVKQRVRVKTVPSLFQAKLDTFLWS

• Sequence length: 469

Pathways

Reactome:

Antigen processing: Ubiquitination & Proteasome degradation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Seckel syndrome 9	Pathogenic; Likely pathogenic	rs767664526, rs864622784, rs761742550	RCV000206973 RCV000206906 RCV003993565	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANXIETY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, HEPATOCELLULAR	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DWARFISM	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEART FAILURE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MICROCEPHALY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SECKEL SYNDROME	—	CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet CTD, Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SUBSTANCE ABUSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRAIP-related disorder	Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Agonadism	Agonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ambiguous Genitalia	Ambiguous Genitalia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	27847407	Inhibit	★☆☆☆☆ Found in Text Mining only
Atrial Septal Defects	Atrial Septal Defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	31972358	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	21068752	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	31972358	Inhibit	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	31972358	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	29975933		★☆☆☆☆ Found in Text Mining only
Chronic myeloproliferative disorder	Myeloproliferative disorder	GENOMICS_ENGLAND_DG	26595769		★☆☆☆☆ Found in Text Mining only
Clinodactyly of the 5th finger	Camptodactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital diaphragmatic hernia	Congenital diaphragmatic hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Craniosynostosis	Craniosynostosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	18200509		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	BEFREE	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dwarfism	Dwarfism	CTD_human_DG	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dwarfism	Dwarfism	Pubtator	26595769	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dwarfism	Dwarfism	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dwarfism	Dwarfism	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FANCONI ANEMIA, COMPLEMENTATION GROUP Q	Fanconi Anemia	GENOMICS_ENGLAND_DG	26595769		★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrichosis	HYPERTRICHOSIS	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertrophy of clitoris	Hypertrophy Of Clitoris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	28069801		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	CTD_human_DG	28284560		★☆☆☆☆ Found in Text Mining only
Lung Diseases, Interstitial	Lung Diseases	BEFREE	30886067		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	29975933		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	30528265		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	32640040	Associate	★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	GENOMICS_ENGLAND_DG	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	CTD_human_DG	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	Pubtator	26595769	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Microcephaly	HPO_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microlissencephaly	Microlissencephaly	CTD_human_DG	26595769		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	19389625		★☆☆☆☆ Found in Text Mining only
Osteoarthritis Knee	Osteoarthritis	Pubtator	37764718	Associate	★☆☆☆☆ Found in Text Mining only
Pituitary dwarfism 1	Pituitary dwarfism	Pubtator	26595769, 37604812	Associate	★☆☆☆☆ Found in Text Mining only
PITUITARY DWARFISM I	Pituitary dwarfism	BEFREE	26595769		★☆☆☆☆ Found in Text Mining only
PITUITARY DWARFISM I	Pituitary dwarfism	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	BEFREE	27271164		★☆☆☆☆ Found in Text Mining only
Scaphycephaly	Scaphocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Seckel syndrome	Seckel Syndrome	GENOMICS_ENGLAND_DG	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seckel syndrome	Seckel Syndrome	ORPHANET_DG	26595769		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seckel syndrome	Seckel Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seckel syndrome	Seckel Syndrome	BEFREE	30165463		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seckel syndrome 1	Seckel syndrome	Pubtator	26595769, 30165463	Associate	★☆☆☆☆ Found in Text Mining only
SECKEL SYNDROME 9	Seckel Syndrome	UNIPROT_DG	26595769		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SECKEL SYNDROME 9	Seckel Syndrome	GENOMICS_ENGLAND_DG	26595769, 30914295		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SECKEL SYNDROME 9	Seckel Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Severe Congenital Microcephaly	Congenital Microcephaly	CTD_human_DG	26595769		★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	18200509		★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only