Is CD55 p.Leu15fs (c.43del) pathogenic?

CD55 p.Leu15fs (c.43del) is classified Pathogenic in CD55 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2017-08-11). Absent from gnomAD; Associated with protein-losing enteropathy.

What condition is associated with CD55 p.Leu15fs (c.43del)?

CD55 p.Leu15fs (c.43del) is associated with protein-losing enteropathy (ClinVar).

How common is CD55 p.Leu15fs (c.43del) in the general population?

CD55 p.Leu15fs (c.43del) is absent from gnomAD (gnomAD).

CD55 p.Leu15fs

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.43del · rs1114167430 · VCV427983

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

protein-losing enteropathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4	GERP -2.8

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: CD55
Protein: p.Leu15fs
Coding: c.43del
MANE Select: NM_000574
dbSNP: rs1114167430
Type: Deletion
Location: chr1:207321807 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB

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 p.Leu15Phe Uncertain significance ★ ⚠ same residue
CD55 p.Leu15= Likely benign ★ same residue
CD55 p.Gly37fs Pathogenic same condition
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

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-leu15fs (accessed [today's date]).

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