Is CD55 p.Met377Val (c.1129A>G) pathogenic?

CD55 p.Met377Val (c.1129A>G) is classified Uncertain significance in CD55 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-05-07). AlphaMissense: likely benign (0.0623); Ultra-rare (popmax 0.0181%, eas); Associated with Inborn genetic diseases.

What condition is associated with CD55 p.Met377Val (c.1129A>G)?

CD55 p.Met377Val (c.1129A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CD55 p.Met377Val (c.1129A>G) in the general population?

CD55 p.Met377Val (c.1129A>G) is ultra-rare (popmax 0.0181%, eas) (gnomAD).

What do computational predictors say about CD55 p.Met377Val (c.1129A>G)?

AlphaMissense predicts likely benign (score 0.0623) — an in-silico prediction, not a clinical call.

CD55 p.Met377Val

c.1129A>G · rs746580979 · VCV1390373

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0623 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0181%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0623	likely benign
REVEL	0.019	moderately benign-leaning
SaProt	LLR -5.51	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 -0.99	GERP -3.5
Regional constraint	o/e 0.90	unconstrained · MANE · 33 kb · p 0.17 · regional, not allelic
Overall
CADD	0.095	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 0.0181% East Asian · 8/44,142 alleles

Filtering AF 0.00896% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0065%

Overall 0.001% 16/1,594,608 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0181%	5,518
South Asian	0.0034%	29,402
Remaining individualsnot grpmax-eligible	0.00324%	30,839
European (non-Finnish)	0.000256%	390,811

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.Met377Val
Coding: c.1129A>G
MANE Select: NM_000574
dbSNP: rs746580979
Type: single nucleotide variant
Location: chr1:207359593 (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.Met377Thr Uncertain significance ★★ ⚠ same residue
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.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-met377val (accessed [today's date]).

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