Is CD55 p.Arg221Ser (c.663A>C) pathogenic?

CD55 p.Arg221Ser (c.663A>C) is classified Uncertain significance in CD55 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-06-29). AlphaMissense: ambiguous (0.4905); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CD55 p.Arg221Ser (c.663A>C)?

CD55 p.Arg221Ser (c.663A>C) is associated with Inborn genetic diseases (ClinVar).

How common is CD55 p.Arg221Ser (c.663A>C) in the general population?

CD55 p.Arg221Ser (c.663A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CD55 p.Arg221Ser (c.663A>C)?

AlphaMissense predicts ambiguous (score 0.4905) — an in-silico prediction, not a clinical call.

CD55 p.Arg221Ser

c.663A>C · rs2102385946 · VCV1385428

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4905 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4905	ambiguous
REVEL	0.099	moderately benign-leaning
SaProt	LLR -11.23	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Regional constraint	o/e 0.90	unconstrained · MANE · 33 kb · p 0.17 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CD55
Protein: p.Arg221Ser
Coding: c.663A>C
MANE Select: NM_000574
dbSNP: rs2102385946
Type: single nucleotide variant
Location: chr1:207326836 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB
Residue 221: the sushi 3 domain; a β-strand

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CD55 p.Asn171Ser Uncertain significance ★★ ⚠ same condition
CD55 p.Asn44Asp Uncertain significance ★★ ⚠ same condition
CD55 p.Glu273Gly Uncertain significance ★★ ⚠ same condition
CD55 p.His339Asn Uncertain significance ★★ ⚠ same condition
CD55 p.Leu374Val Uncertain significance ★★ ⚠ same condition
CD55 p.Met377Thr Uncertain significance ★★ ⚠ same condition
CD55 p.Met377Val Uncertain significance ★★ ⚠ same condition
CD55 p.Pro166Leu Uncertain significance ★★ 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-arg221ser (accessed [today's date]).

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