Is CD55 p.Leu82Arg (c.245T>G) pathogenic?

CD55 p.Leu82Arg (c.245T>G) is classified Likely benign in CD55 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-04-03). AlphaMissense: likely benign (0.0917); Rare (popmax 0.354%, afr).

How common is CD55 p.Leu82Arg (c.245T>G) in the general population?

CD55 p.Leu82Arg (c.245T>G) is rare (popmax 0.354%, afr) (gnomAD).

What do computational predictors say about CD55 p.Leu82Arg (c.245T>G)?

AlphaMissense predicts likely benign (score 0.0917) — an in-silico prediction, not a clinical call.

CD55 p.Leu82Arg

c.245T>G · rs147474393 · VCV1150714

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0917 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.354%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0917	likely benign
REVEL	0.11	moderately benign-leaning
SaProt	LLR -7.37	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.26	GERP -3
Regional constraint	o/e 1.17	unconstrained · MANE · 761 bp · p 0.08 · regional, not allelic
Overall
CADD	13.59	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

Grpmax group 0.354% African / African-American · 266/75,052 alleles

Filtering AF 0.319% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.306%

Overall 0.0318% 514/1,614,078 alleles · rare exomes 315/1,461,710 · genomes 199/152,368 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.354%	282
Finnishnot grpmax-eligible	0.344%	291
Remaining individualsnot grpmax-eligible	0.0176%	5,682
Admixed American	0.01%	9,998
East Asian	0.00446%	22,443
European (non-Finnish)	0.000763%	131,110

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.Leu82Arg
Coding: c.245T>G
MANE Select: NM_000574
dbSNP: rs147474393
Type: single nucleotide variant
Location: chr1:207322526 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB
Residue 82: a UniProt-annotated variant site (in wes(a) antigen); the sushi 1 domain; a β-strand

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

Similar variants

CD55 c.286+1G>A Likely pathogenic ★★ same type
CD55 c.286+2T>G Likely pathogenic ★★ same type
CD55 p.Glu50Ter Pathogenic/Likely pathogenic ★★ same type
CD55 p.Trp213Ter Pathogenic/Likely pathogenic ★★ same type
CD55 c.1081+1G>C Uncertain significance ★★ same type
CD55 p.Arg221Ser Uncertain significance ★★ ⚠ same type
CD55 p.Arg357Cys Uncertain significance ★★ ⚠ same type
CD55 p.Arg357His 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/cd55-p-leu82arg (accessed [today's date]).

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