Is PDE6B p.Pro41fs (c.121_125del) pathogenic?

PDE6B p.Pro41fs (c.121125del) is classified Pathogenic in PDE6B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2014-03-13). Absent from gnomAD; Associated with Autosomal recessive retinitis pigmentosa.

What condition is associated with PDE6B p.Pro41fs (c.121_125del)?

PDE6B p.Pro41fs (c.121_125del) is associated with Autosomal recessive retinitis pigmentosa (ClinVar).

How common is PDE6B p.Pro41fs (c.121_125del) in the general population?

PDE6B p.Pro41fs (c.121_125del) is absent from gnomAD (gnomAD).

PDE6B p.Pro41fs

c.121_125del · rs1734056711 · VCV978977

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Autosomal recessive retinitis pigmentosa

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 1 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.8	GERP -3.7

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: PDE6B
Protein: p.Pro41fs
Coding: c.121_125del
MANE Select: NM_000283
dbSNP: rs1734056711
Type: Deletion
Location: chr4:625746 (GRCh38)
Gene constraint: LOEUF 1.238 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.72

Full PDE6B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Autosomal recessive retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PDE6B p.Pro41Arg Uncertain significance ★ ⚠ same residue
PDE6B p.Pro41= Likely benign ★ same residue
PDE6B p.Pro41Leu Likely benign ★ same residue
PDE6B c.2353-18_2354del Pathogenic/Likely pathogenic ★★ same type
PDE6B p.Ala143fs Pathogenic ★★ same type
PDE6B p.Arg82fs Pathogenic ★★ same type
PDE6B p.Asn643fs Pathogenic/Likely pathogenic ★★ same type
PDE6B p.Asp252fs Pathogenic/Likely 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/pde6b-p-pro41fs (accessed [today's date]).

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