Is PDE6A p.Leu769fs (c.2306del) pathogenic?

PDE6A p.Leu769fs (c.2306del) is classified Pathogenic in PDE6A (ClinVar, Single submitter, 1 submitter; last evaluated 2022-06-20). Absent from gnomAD.

How common is PDE6A p.Leu769fs (c.2306del) in the general population?

PDE6A p.Leu769fs (c.2306del) is absent from gnomAD (gnomAD).

PDE6A p.Leu769fs

c.2306del · rs2113503448 · VCV1457627

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 20 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP -1.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: PDE6A
Protein: p.Leu769fs
Coding: c.2306del
MANE Select: NM_000440
dbSNP: rs2113503448
Type: Deletion
Location: chr5:149866222 (GRCh38)
Gene constraint: LOEUF 0.888 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.80
Residue 769: the pdease domain

Full PDE6A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PDE6A p.Arg707fs Pathogenic/Likely pathogenic ★★ same type
PDE6A p.Asp366fs Likely pathogenic ★★ same type
PDE6A p.Asp778fs Pathogenic/Likely pathogenic ★★ same type
PDE6A p.Leu96fs Pathogenic/Likely pathogenic ★★ same type
PDE6A p.Phe97fs Pathogenic/Likely pathogenic ★★ same type
PDE6A p.Ser422_Leu423insTer Pathogenic ★★ same type
PDE6A p.Thr679fs Pathogenic/Likely pathogenic ★★ same type
PDE6A p.Tyr275fs Pathogenic ★★ 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/pde6a-p-leu769fs (accessed [today's date]).

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