Is CD59 c.169+9del pathogenic?

CD59 c.169+9del is classified Likely benign in CD59 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-08). Very rare (popmax 0.000141%).

How common is CD59 c.169+9del in the general population?

CD59 c.169+9del is very rare (popmax 0.000141%) (gnomAD).

CD59 c.169+9del

rs1368231179 · VCV3011349

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000141%)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +9	near-intronic (+9 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1	GERP -1.9
Non-coding constraint	Z 0.36	1 kb window · o/e 0.97 · regional · uncalibrated

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000141%

Overall 0.000141% 2/1,420,376 alleles · very rare

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: CD59
Coding: c.169+9del
MANE Select: NM_000611
dbSNP: rs1368231179
Type: Deletion
Location: chr11:33717361 (GRCh38)
Gene constraint: LOEUF 1.277 · pLI 0.57 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.15 · 17 PDB

Full CD59 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD59 p.Asp47_Phe48insTer Likely pathogenic ★ same type
CD59 p.Cys64fs Likely pathogenic ★ same type
CD59 p.Glu101fs Likely pathogenic ★ same type
CD59 p.Leu93_Cys94insTer Likely pathogenic ★ same type
CD59 p.Phe96fs Uncertain significance ★ same type
CD59 c.169+14_169+15del Likely benign ★ same type
CD59 c.169+15del Likely benign ★ same type
CD59 c.68-15del Likely benign ★ 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/cd59-c-169-plus-9del (accessed [today's date]).

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