Is CD55 p.Thr363= (c.1089G>A) pathogenic?

CD55 p.Thr363= (c.1089G>A) is classified Conflicting classifications of pathogenicity in CD55 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-08-09). Very rare (popmax 0.00781%, afr); Associated with Inborn genetic diseases.

What condition is associated with CD55 p.Thr363= (c.1089G>A)?

CD55 p.Thr363= (c.1089G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CD55 p.Thr363= (c.1089G>A) in the general population?

CD55 p.Thr363= (c.1089G>A) is very rare (popmax 0.00781%, afr) (gnomAD).

CD55 p.Thr363=

c.1089G>A · rs767750936 · VCV1537548

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00781%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.015	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.3	GERP -3.5
Overall
CADD	2.503	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00781% African / African-American · 5/63,982 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00196%

Overall 0.00127% 19/1,499,384 alleles · very rare exomes 15/1,369,484 · genomes 4/129,900 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00781%	12,796
South Asian	0.00361%	27,733
Finnishnot grpmax-eligible	0.00182%	54,946
Remaining individualsnot grpmax-eligible	0.00173%	57,750
European (non-Finnish)	0.000807%	123,909

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.Thr363=
Coding: c.1089G>A
MANE Select: NM_000574
dbSNP: rs767750936
Type: single nucleotide variant
Location: chr1:207359553 (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

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

Similar variants

CD55 p.Arg221Ser Uncertain significance ★★ ⚠ same condition
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

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-thr363 (accessed [today's date]).

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