Is CD55 p.Glu239= (c.717A>G) pathogenic?

CD55 p.Glu239= (c.717A>G) is classified Likely benign in CD55 (ClinVar, Single submitter, 1 submitter). Very rare (popmax 6.84e-05%); Associated with protein-losing enteropathy.

What condition is associated with CD55 p.Glu239= (c.717A>G)?

CD55 p.Glu239= (c.717A>G) is associated with protein-losing enteropathy (ClinVar).

How common is CD55 p.Glu239= (c.717A>G) in the general population?

CD55 p.Glu239= (c.717A>G) is very rare (popmax 6.84e-05%) (gnomAD).

CD55 p.Glu239=

Q: How is Complement hyperactivation-angiopathic thrombosis-protein-losing enteropathy syndrome inherited?

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

c.717A>G · rs1654924770 · VCV2500014

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 6.84e-05%)

Conditions

protein-losing enteropathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.048	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.3	GERP -2
Overall
CADD	2.351	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.84e-05%

Overall 6.84e-05% 1/1,461,468 alleles · very rare

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: CD55
Protein: p.Glu239=
Coding: c.717A>G
MANE Select: NM_000574
dbSNP: rs1654924770
Type: single nucleotide variant
Location: chr1:207331160 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB
Residue 239: a disulfide bond; the sushi 4 domain

Full CD55 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

protein-losing enteropathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Complement hyperactivation-angiopathic thrombosis-protein-losing enteropathy syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

CD55 c.286+2T>G Likely pathogenic ★★ same condition
CD55 p.Glu50Ter Pathogenic/Likely pathogenic ★★ same condition
CD55 c.1081+1G>C Uncertain significance ★★ same condition
CD55 p.Arg357Cys Uncertain significance ★★ ⚠ same condition
CD55 p.Arg52Leu Benign/Likely benign ★★ ⚠ same condition
CD55 p.Cys267Ser Pathogenic ★ same condition
CD55 p.Ser199Leu Pathogenic ★ ⚠ same condition
CD55 p.Trp33Ter 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/cd55-p-glu239 (accessed [today's date]).

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