TRAFD1

TRAF-type zinc finger domain containing 1

Basic information

Region (hg38): 12:112125538-112153604

Links

ENSG00000135148NCBI:10906OMIM:613197HGNC:24808Uniprot:O14545AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAFD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAFD1 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
clinvar
1
missense
25
clinvar
3
clinvar
28
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 25 3 1

Variants in TRAFD1

This is a list of pathogenic ClinVar variants found in the TRAFD1 region.

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

Position Type Phenotype Significance ClinVar
12-112130551-C-A not specified Uncertain significance (Mar 24, 2023)2529768
12-112134802-A-G not specified Likely benign (Dec 27, 2023)3181804
12-112134848-C-G not specified Uncertain significance (Feb 27, 2024)3181807
12-112134856-G-A not specified Uncertain significance (May 17, 2023)2570273
12-112135026-G-T not specified Uncertain significance (Nov 14, 2023)3181808
12-112140903-T-G not specified Uncertain significance (Mar 30, 2022)2280989
12-112140975-C-G not specified Uncertain significance (Jun 21, 2022)2296102
12-112140978-G-C not specified Uncertain significance (Sep 26, 2023)3181809
12-112140995-G-C not specified Likely benign (Oct 27, 2023)3181810
12-112141016-G-C not specified Uncertain significance (Aug 09, 2021)2226901
12-112141086-C-T not specified Uncertain significance (Dec 01, 2022)2378926
12-112142141-G-A Benign (Jul 23, 2018)788439
12-112142245-G-A not specified Uncertain significance (May 11, 2022)2376215
12-112142268-G-A not specified Uncertain significance (Jun 06, 2023)2520925
12-112148197-G-C not specified Uncertain significance (Jan 11, 2023)2475777
12-112151825-A-G not specified Uncertain significance (Jan 10, 2023)2459061
12-112151875-A-G not specified Uncertain significance (Aug 16, 2022)2388407
12-112151881-C-T not specified Uncertain significance (Nov 15, 2021)2402420
12-112151882-C-G not specified Uncertain significance (Mar 18, 2024)2227506
12-112151927-C-T not specified Uncertain significance (May 24, 2023)2551811
12-112151941-C-G not specified Uncertain significance (Oct 16, 2023)3181805
12-112152011-G-A not specified Likely benign (Sep 17, 2021)2366780
12-112152017-G-A not specified Uncertain significance (Apr 04, 2024)3328443
12-112152035-C-T not specified Uncertain significance (May 02, 2024)3328440
12-112152046-G-A not specified Uncertain significance (Oct 26, 2022)2206916

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TRAFD1protein_codingprotein_codingENST00000257604 1128103
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.94e-80.9671257010461257470.000183
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6152923230.9040.00001673841
Missense in Polyphen721040.692321291
Synonymous1.71951190.8000.000005961116
Loss of Function2.081729.10.5840.00000152327

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001480.000148
Ashkenazi Jewish0.000.00
East Asian0.0004360.000435
Finnish0.00009240.0000924
European (Non-Finnish)0.0002110.000211
Middle Eastern0.0004360.000435
South Asian0.0002610.000261
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Negative feedback regulator that controls excessive innate immune responses. Regulates both Toll-like receptor 4 (TLR4) and DDX58/RIG1-like helicases (RLH) pathways. May inhibit the LTR pathway by direct interaction with TRAF6 and attenuation of NF-kappa-B activation. May negatively regulate the RLH pathway downstream from MAVS and upstream of NF-kappa-B and IRF3 (By similarity). {ECO:0000250, ECO:0000269|PubMed:16221674}.;
Pathway
Regulation of toll-like receptor signaling pathway (Consensus)

Recessive Scores

pRec
0.0982

Intolerance Scores

loftool
0.921
rvis_EVS
-0.2
rvis_percentile_EVS
38.98

Haploinsufficiency Scores

pHI
0.0710
hipred
N
hipred_score
0.169
ghis
0.531

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.000571

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Trafd1
Phenotype
immune system phenotype; growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);

Gene ontology

Biological process
negative regulation of innate immune response
Cellular component
Molecular function
protein binding;metal ion binding