Is PDE6C p.Ala599del (c.1789GCT[2]) pathogenic?

PDE6C p.Ala599del (c.1789GCT[2]) is classified Uncertain significance in PDE6C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-10). Absent from gnomAD v4.1.

How common is PDE6C p.Ala599del (c.1789GCT[2]) in the general population?

PDE6C p.Ala599del (c.1789GCT[2]) is absent from gnomAD v4.1 (gnomAD).

PDE6C p.Ala599del

c.1789GCT[2] · rs2058556950 · VCV1382898

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,634)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 2.2, phastCons 1

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,634). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PDE6C
Protein: p.Ala599del
Coding: c.1789GCT[2]
MANE Select: NM_006204
dbSNP: rs2058556950
Type: Microsatellite
Location: chr10:93640970 (GRCh38)
Gene constraint: LOEUF 0.976 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.53 · 7 PDB
Residue 599: a UniProt-annotated variant site (in achm5); the pdease domain; an α-helix

Full PDE6C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PDE6C p.Thr709fs Pathogenic/Likely pathogenic ★★ same type
PDE6C p.Glu699del Uncertain significance ★★ same type
PDE6C p.Glu834del Uncertain significance ★★ same type
PDE6C p.Cys784fs Likely pathogenic ★ same type
PDE6C p.Leu641fs Pathogenic ★ same type
PDE6C p.Leu87fs Pathogenic ★ same type
PDE6C p.Phe136fs Pathogenic ★ same type
PDE6C c.940-14TCTT[2] Conflicting classifications of pathogenicity ★ 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/pde6c-p-ala599del (accessed [today's date]).

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