Is CD55 p.Thr373= (c.1119G>A) pathogenic?

CD55 p.Thr373= (c.1119G>A) is classified Likely benign in CD55 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-10). Very rare (popmax 0.00228%, sas); Associated with Inborn genetic diseases.

What condition is associated with CD55 p.Thr373= (c.1119G>A)?

CD55 p.Thr373= (c.1119G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CD55 p.Thr373= (c.1119G>A) in the general population?

CD55 p.Thr373= (c.1119G>A) is very rare (popmax 0.00228%, sas) (gnomAD).

CD55 p.Thr373=

c.1119G>A · VCV3829593

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00228%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.115	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -0.064, phastCons 0.92
Overall
CADD	6.148	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00228% South Asian · 2/87,910 alleles

Filtering AF 0.000378% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000141%

Overall 0.000277% 4/1,442,896 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00228%	43,955
European (non-Finnish)	0.000171%	585,251

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.Thr373=
Coding: c.1119G>A
MANE Select: NM_000574
Type: single nucleotide variant
Location: chr1:207359583 (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.Thr373Met 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.Met377Thr 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-thr373 (accessed [today's date]).

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