Is CD52 p.Phe4= (c.12C>T) pathogenic?

CD52 p.Phe4= (c.12C>T) is classified Likely benign in CD52 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-18). Ultra-rare (popmax 0.0156%, eas); Associated with CD52-related disorder.

What condition is associated with CD52 p.Phe4= (c.12C>T)?

CD52 p.Phe4= (c.12C>T) is associated with CD52-related disorder (ClinVar).

How common is CD52 p.Phe4= (c.12C>T) in the general population?

CD52 p.Phe4= (c.12C>T) is ultra-rare (popmax 0.0156%, eas) (gnomAD).

CD52 p.Phe4=

c.12C>T · rs371901792 · VCV3057395

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0156%, eas)

Conditions

CD52-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.4	GERP 0.88, phastCons 0.012
Overall
CADD	7.981	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0156% East Asian · 7/44,892 alleles

Filtering AF 0.00726% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00514%

Overall 0.000743% 12/1,614,206 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0156%	6,413
Remaining individualsnot grpmax-eligible	0.0032%	31,255
Admixed American	0.00167%	60,018
European (non-Finnish)	0.000169%	590,009

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: CD52
Protein: p.Phe4=
Coding: c.12C>T
MANE Select: NM_001803
dbSNP: rs371901792
Type: single nucleotide variant
Location: chr1:26318029 (GRCh38)
Gene constraint: LOEUF 1.787 · pLI 0.12 (gnomAD)
Structure: AlphaFold pLDDT 68.22 · 1 PDB

Full CD52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD52-related disorder

Similar variants

CD52 p.Asn40Ser Benign same condition
CD52 p.Ile41Met Benign ⚠ same condition
CD52 p.Arg3Cys Uncertain significance ★ ⚠ same type
CD52 p.Cys59Gly Uncertain significance ★ ⚠ same type
CD52 p.Gly43Arg Uncertain significance ★ ⚠ same type
CD52 p.Ile11Val Uncertain significance ★ ⚠ same type
CD52 p.Leu5Val Uncertain significance ★ ⚠ same type
CD52 p.Met16Thr Uncertain significance ★ ⚠ same type

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/cd52-p-phe4 (accessed [today's date]).

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