Is CD70 p.Phe186del (c.552CTT[1]) pathogenic?

CD70 p.Phe186del (c.552CTT[1]) is classified Pathogenic in CD70 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-01-10). Absent from gnomAD; Associated with severe combined immunodeficiency due to CD70 deficiency.

What condition is associated with CD70 p.Phe186del (c.552CTT[1])?

CD70 p.Phe186del (c.552CTT[1]) is associated with severe combined immunodeficiency due to CD70 deficiency (ClinVar).

How common is CD70 p.Phe186del (c.552CTT[1]) in the general population?

CD70 p.Phe186del (c.552CTT[1]) is absent from gnomAD (gnomAD).

CD70 p.Phe186del

Q: How is EBV-induced lymphoproliferative disease due to CD70 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.552CTT[1] · rs1568431102 · VCV599339

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

severe combined immunodeficiency due to CD70 deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.045	GERP -0.68, phastCons 0.21

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CD70
Protein: p.Phe186del
Coding: c.552CTT[1]
MANE Select: NM_001252
dbSNP: rs1568431102
Type: Microsatellite
Location: chr19:6586045 (GRCh38)
Gene constraint: LOEUF 1.251 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 83.52 · 1 PDB
Residue 186: a UniProt-annotated variant site (in lpfs3; loss of protein expression); a UniProt-annotated variant site (in lpfs3; no effect on protein expression; loss of interaction with cd27); the thd domain; a β-strand

Full CD70 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

severe combined immunodeficiency due to CD70 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For EBV-induced lymphoproliferative disease due to CD70 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

CD70 p.Arg179Ter Pathogenic same condition
CD70 p.Ser84fs Pathogenic same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cd70-p-phe186del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown