Is CD27 p.Cys10= (c.30C>T) pathogenic?

CD27 p.Cys10= (c.30C>T) is classified Benign/Likely benign in CD27 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-27). Low-frequency (popmax 3.18%, afr); Associated with autoinflammatory syndrome.

What condition is associated with CD27 p.Cys10= (c.30C>T)?

CD27 p.Cys10= (c.30C>T) is associated with autoinflammatory syndrome, lymphoproliferative syndrome 2 (ClinVar).

How common is CD27 p.Cys10= (c.30C>T) in the general population?

CD27 p.Cys10= (c.30C>T) is low-frequency (popmax 3.18%, afr) (gnomAD).

CD27 p.Cys10=

c.30C>T · rs34540052 · VCV473872

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.18%, afr)

Conditions

autoinflammatory syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.2	GERP -3, phastCons 0.004
Overall
CADD	10.41	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.18% African / African-American · 2,378/74,810 alleles

Filtering AF 3.07% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.03%

Overall 0.161% 2,580/1,606,138 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.18%	31
Remaining individualsnot grpmax-eligible	0.159%	628
Admixed American	0.124%	805
Middle Eastern	0.0514%	1,944
South Asian	0.00222%	44,979
European (non-Finnish)	0.00221%	45,269

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CD27
Protein: p.Cys10=
Coding: c.30C>T
dbSNP: rs34540052
Type: single nucleotide variant
Location: chr12:6445125 (GRCh38)

Full CD27 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autoinflammatory syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: lymphoproliferative syndrome 2

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/cd27-p-cys10 (accessed [today's date]).

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