CD70

CD70 molecule, the group of CD molecules|Tumor necrosis factor superfamily

Basic information

Region (hg38): 19:6583183-6604103

Previous symbols: [ "CD27LG", "TNFSF7" ]

Links

ENSG00000125726NCBI:970OMIM:602840HGNC:11937Uniprot:P32970AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Lymphoproliferative syndrome 3ARAllergy/Immunology/Infectious; OncologicSome 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 diseaseAllergy/Immunology/Infectious; Oncologic28011863; 28011864

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD70 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
4
missense
25
clinvar
2
clinvar
27
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
0
Total 2 0 26 6 0

Highest pathogenic variant AF is 0.0000027365

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CD70protein_codingprotein_codingENST00000245903 320921
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01040.629125736021257380.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.802971220.7960.000007141211
Missense in Polyphen2344.1870.52052366
Synonymous0.6694753.20.8830.00000274443
Loss of Function0.38333.810.7881.63e-741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001790.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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