TRAF3IP1

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 26487268

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRAF3IP1 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 19

Senior-Loken syndrome 9Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	122 clinvar	6 clinvar	129
missense			253 clinvar	9 clinvar	6 clinvar	268
nonsense	6 clinvar					6
start loss						0
frameshift	12 clinvar	1 clinvar	4 clinvar			17
splice donor/acceptor (+/-2bp)	1 clinvar	9 clinvar	1 clinvar	2 clinvar		13
Total	19	10	259	133	12	433

Highest pathogenic variant AF is 0.0000460211

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
traf3ip1	Danio rerio	Structure: neuromast hair cell Quality: absent abnormal

Gene / Model

Organism

Observed Phenotype

traf3ip1

Danio rerio

Structure: neuromast hair cell

Quality: absent

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Intraflagellar transport
Cilium Assembly
Organelle biogenesis and maintenance

Biological Process

morphogenesis of a polarized epithelium
kidney development
negative regulation of protein phosphorylation
neural tube patterning
embryonic camera-type eye development

Molecular Function

protein binding
microtubule binding

Cellular Component

centrosome
cilium
axoneme
intraciliary transport particle B
ciliary transition zone

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373327
Coding exons: 17
Length: 80460
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125748
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.328	346	364	0.952	0.0000205	4507
Missense (PolyPhen)		73	95.424	0.76501		1202
Synonymous	-0.297	145	141	1.03	0.00000869	1250
Loss of Function	2.83	19	37.8	0.503	0.00000206	491

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00019	0.00017	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00017	0.00016	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00027	0.00026	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays an inhibitory role on IL13 signaling by binding to IL13RA1. Involved in suppression of IL13-induced STAT6 phosphorylation, transcriptional activity and DNA-binding. Recruits TRAF3 and DISC1 to the microtubules. Involved in kidney development and epithelial morphogenesis. Involved in the regulation of microtubule cytoskeleton organization. Is a negative regulator of microtubule stability, acting through the control of MAP4 levels (PubMed:26487268). Involved in ciliogenesis (By similarity). {ECO:0000250|UniProtKB:Q149C2, ECO:0000269|PubMed:10791955, ECO:0000269|PubMed:12812986, ECO:0000269|PubMed:12935900, ECO:0000269|PubMed:26487268}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.907
RVIS EVS: 0.96
RVIS percentile EVS: 90.17

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.407

Gene Damage Prediction

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