CD70
Basic information
Region (hg38): 19:6583183-6604103
Previous symbols: [ "CD27LG", "TNFSF7" ]
Links
Phenotypes
GenCC
Source:
- severe combined immunodeficiency due to CD70 deficiency (Moderate), mode of inheritance: AR
- severe combined immunodeficiency due to CD70 deficiency (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Lymphoproliferative syndrome 3 | AR | Allergy/Immunology/Infectious; Oncologic | Some individuals may patients may have recurrent infections, and awareness may allow prophylactic measures and prompt and aggressive management of infections; Individuals have been described as having increased susceptibility to Epstein-Barr virus infection, causing increased risk of B-cell malignancies, and awareness may allow prompt diagnosis and management of oncologic disease | Allergy/Immunology/Infectious; Oncologic | 28011863; 28011864 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (22 variants)
- not_provided (8 variants)
- CD70-related_disorder (4 variants)
- Severe_combined_immunodeficiency_due_to_CD70_deficiency (3 variants)
- not_specified (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD70 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001252.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 25 | 27 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 2 | 0 | 26 | 6 | 0 |
Highest pathogenic variant AF is 0.0000027365
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CD70 | protein_coding | protein_coding | ENST00000245903 | 3 | 20921 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0104 | 0.629 | 125736 | 0 | 2 | 125738 | 0.00000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.802 | 97 | 122 | 0.796 | 0.00000714 | 1211 |
Missense in Polyphen | 23 | 44.187 | 0.52052 | 366 | ||
Synonymous | 0.669 | 47 | 53.2 | 0.883 | 0.00000274 | 443 |
Loss of Function | 0.383 | 3 | 3.81 | 0.788 | 1.63e-7 | 41 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000179 | 0.0000176 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cytokine that binds to CD27. Plays a role in T-cell activation. Induces the proliferation of costimulated T-cells and enhances the generation of cytolytic T-cells.;
- Pathway
- Cytokine-cytokine receptor interaction - Homo sapiens (human);TNFR2 non-canonical NF-kB pathway;Cytokine Signaling in Immune system;Immune System;TNFs bind their physiological receptors
(Consensus)
Recessive Scores
- pRec
- 0.215
Intolerance Scores
- loftool
- 0.259
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.105
- hipred
- N
- hipred_score
- 0.188
- ghis
- 0.629
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.184
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cd70
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- immune response;signal transduction;cell-cell signaling;cell population proliferation;regulation of signaling receptor activity;tumor necrosis factor-mediated signaling pathway;extrinsic apoptotic signaling pathway
- Cellular component
- plasma membrane;integral component of plasma membrane;extracellular exosome
- Molecular function
- protease binding;signaling receptor binding;cytokine activity;tumor necrosis factor receptor binding;protein binding