Is CD55 p.Pro112Ser (c.334C>T) pathogenic?

CD55 p.Pro112Ser (c.334C>T) is classified Uncertain significance in CD55 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-20). AlphaMissense: likely benign (0.1824); Very rare (popmax 0.00838%, amr); Associated with Inborn genetic diseases.

What condition is associated with CD55 p.Pro112Ser (c.334C>T)?

CD55 p.Pro112Ser (c.334C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CD55 p.Pro112Ser (c.334C>T) in the general population?

CD55 p.Pro112Ser (c.334C>T) is very rare (popmax 0.00838%, amr) (gnomAD).

What do computational predictors say about CD55 p.Pro112Ser (c.334C>T)?

AlphaMissense predicts likely benign (score 0.1824) — an in-silico prediction, not a clinical call.

CD55 p.Pro112Ser

c.334C>T · VCV3998281

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1824 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00838%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1824	likely benign
REVEL	0.064	moderately benign-leaning
SaProt	LLR -6.23	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.52 · evaluated, not missing
Constraint at this position
Conservation	phyloP -3.7	GERP -4.3
Regional constraint	o/e 0.68	unconstrained · MANE · 4,298 bp · p 4.2e-05 · regional, not allelic
Overall
CADD	0.003	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00838% Admixed American · 5/59,680 alleles

Filtering AF 0.00325% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00208%

Overall 0.000434% 7/1,611,480 alleles · very rare exomes 7/1,459,240 · genomes 0/152,240 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00838%	11,936
East Asian	0.00223%	44,794
European (non-Finnish)	8.48e-05%	1,178,766

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.Pro112Ser
Coding: c.334C>T
MANE Select: NM_000574
Type: single nucleotide variant
Location: chr1:207324606 (GRCh38)
Gene constraint: LOEUF 1.234 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.99 · 33 PDB
Residue 112: the sushi 2 domain

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-pro112ser (accessed [today's date]).

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