TRAFD1
Basic information
Region (hg38): 12:112125538-112153604
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 25 | 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) | ||
12-112134802-A-G | not specified | Likely benign (Dec 27, 2023) | ||
12-112134848-C-G | not specified | Uncertain significance (Feb 27, 2024) | ||
12-112134856-G-A | not specified | Uncertain significance (May 17, 2023) | ||
12-112135026-G-T | not specified | Uncertain significance (Nov 14, 2023) | ||
12-112140903-T-G | not specified | Uncertain significance (Mar 30, 2022) | ||
12-112140975-C-G | not specified | Uncertain significance (Jun 21, 2022) | ||
12-112140978-G-C | not specified | Uncertain significance (Sep 26, 2023) | ||
12-112140995-G-C | not specified | Likely benign (Oct 27, 2023) | ||
12-112141016-G-C | not specified | Uncertain significance (Aug 09, 2021) | ||
12-112141086-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
12-112142141-G-A | Benign (Jul 23, 2018) | |||
12-112142245-G-A | not specified | Uncertain significance (May 11, 2022) | ||
12-112142268-G-A | not specified | Uncertain significance (Jun 06, 2023) | ||
12-112148197-G-C | not specified | Uncertain significance (Jan 11, 2023) | ||
12-112151825-A-G | not specified | Uncertain significance (Jan 10, 2023) | ||
12-112151875-A-G | not specified | Uncertain significance (Aug 16, 2022) | ||
12-112151881-C-T | not specified | Uncertain significance (Nov 15, 2021) | ||
12-112151882-C-G | not specified | Uncertain significance (Mar 18, 2024) | ||
12-112151927-C-T | not specified | Uncertain significance (May 24, 2023) | ||
12-112151941-C-G | not specified | Uncertain significance (Oct 16, 2023) | ||
12-112152011-G-A | not specified | Likely benign (Sep 17, 2021) | ||
12-112152017-G-A | not specified | Uncertain significance (Apr 04, 2024) | ||
12-112152035-C-T | not specified | Uncertain significance (May 02, 2024) | ||
12-112152046-G-A | not specified | Uncertain significance (Oct 26, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TRAFD1 | protein_coding | protein_coding | ENST00000257604 | 11 | 28103 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.94e-8 | 0.967 | 125701 | 0 | 46 | 125747 | 0.000183 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.615 | 292 | 323 | 0.904 | 0.0000167 | 3841 |
Missense in Polyphen | 72 | 104 | 0.69232 | 1291 | ||
Synonymous | 1.71 | 95 | 119 | 0.800 | 0.00000596 | 1116 |
Loss of Function | 2.08 | 17 | 29.1 | 0.584 | 0.00000152 | 327 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000148 | 0.000148 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000436 | 0.000435 |
Finnish | 0.0000924 | 0.0000924 |
European (Non-Finnish) | 0.000211 | 0.000211 |
Middle Eastern | 0.000436 | 0.000435 |
South Asian | 0.000261 | 0.000261 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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