CD70

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

Basic information

Region (hg38): 19:6583183-6604103

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

Links

ENSG00000125726 ∙ NCBI:970 ∙ OMIM:602840 ∙ HGNC:11937 ∙ Uniprot:P32970 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			25	2		27
nonsense	1					1
start loss						0
frameshift	1		1			2
splice donor/acceptor (+/-2bp)						0
Total	2	0	26	6	0

Highest pathogenic variant AF is 0.0000027365

GnomAD

Source: gnomAD

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: 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

	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