Is PDE6A p.Glu808= (c.2424G>A) pathogenic?

PDE6A p.Glu808= (c.2424G>A) is classified Benign in PDE6A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-02-01). Common (popmax 13.8%, afr) — too common for a highly-penetrant pathogenic allele; Associated with retinitis pigmentosa.

What condition is associated with PDE6A p.Glu808= (c.2424G>A)?

PDE6A p.Glu808= (c.2424G>A) is associated with retinitis pigmentosa (ClinVar).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PDE6A p.Glu808=

Q: How common is PDE6A p.Glu808= (c.2424G>A) in the general population?

PDE6A p.Glu808= (c.2424G>A) is common (popmax 13.8%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2424G>A · rs10067462 · VCV351981

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Common

common (popmax 13.8%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

retinitis pigmentosa

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.25	GERP -4.2, phastCons 0.98
Overall
CADD	5.906	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 13.8% African / African-American · 10,355/74,992 alleles

Filtering AF 13.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 13.5%

Overall 0.874% 14,109/1,614,138 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	13.8%	7
Remaining individualsnot grpmax-eligible	1.27%	79
Middle Eastern	1.22%	82
Admixed American	1.04%	96
South Asian	0.733%	136
Ashkenazi Jewishnot grpmax-eligible	0.51%	196
European (non-Finnish)	0.122%	821
Finnishnot grpmax-eligible	0.00781%	12,808
East Asian	0.00446%	22,440

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: PDE6A
Protein: p.Glu808=
Coding: c.2424G>A
MANE Select: NM_000440
dbSNP: rs10067462
Type: single nucleotide variant
Location: chr5:149863201 (GRCh38)
Gene constraint: LOEUF 0.888 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.80
Residue 808: the pdease domain

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

Disease context

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

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

PDE6A c.1065+2T>A Pathogenic/Likely pathogenic ★★ same condition
PDE6A c.1620+1G>A Pathogenic ★★ same condition
PDE6A c.1926+1G>A Pathogenic ★★ same condition
PDE6A c.1927-1G>C Pathogenic/Likely pathogenic ★★ same condition
PDE6A c.627+2T>G Pathogenic ★★ same condition
PDE6A c.998+1G>A Pathogenic ★★ same condition
PDE6A p.Arg102Cys Pathogenic/Likely pathogenic ★★ same condition
PDE6A p.Arg257Ter Pathogenic/Likely pathogenic ★★ 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/pde6a-p-glu808 (accessed [today's date]).

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