Is CD55 p.Lys347Glu (c.1039A>G) pathogenic?

CD55 p.Lys347Glu (c.1039A>G) is classified Benign in CD55 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-01). AlphaMissense: likely benign (0.0794); Very rare (popmax 0.00512%, nfe).

How common is CD55 p.Lys347Glu (c.1039A>G) in the general population?

CD55 p.Lys347Glu (c.1039A>G) is very rare (popmax 0.00512%, nfe) (gnomAD).

What do computational predictors say about CD55 p.Lys347Glu (c.1039A>G)?

AlphaMissense predicts likely benign (score 0.0794) — an in-silico prediction, not a clinical call.

CD55 p.Lys347Glu

c.1039A>G · rs142809668 · VCV726239

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0794 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00512%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0794	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -6.28	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 0.072	GERP -1.3
Regional constraint	o/e 0.90	unconstrained · MANE · 33 kb · p 0.17 · regional, not allelic
Overall
CADD	10.42	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 0.00512% European (non-Finnish) · 60/1,172,280 alleles

Filtering AF 0.00404% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00364%

Overall 0.0261% 419/1,605,430 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	1.05%	96
Remaining individualsnot grpmax-eligible	0.0772%	1,296
European (non-Finnish)grpmax	0.00512%	19,538
Admixed American	0.00167%	59,970
African / African-American	0.00134%	74,716

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Lys347Glu
Coding: c.1039A>G
MANE Select: NM_000574
dbSNP: rs142809668
Type: single nucleotide variant
Location: chr1:207337388 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB
Residue 347: the 'disordered' region

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

Similar variants

CD55 p.Lys347Arg Uncertain significance ★ ⚠ same residue
CD55 p.Lys347Gln Uncertain significance ★ ⚠ same residue
CD55 p.Lys347= Likely benign ★ same residue
CD55 p.Lys347fs Uncertain significance ★★ same residue
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

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-lys347glu (accessed [today's date]).

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