Is PDE6A p.Asp800= (c.2400C>T) pathogenic?

PDE6A p.Asp800= (c.2400C>T) is classified Benign in PDE6A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-02). Common (popmax 10.3%, amr) — too common for a highly-penetrant pathogenic allele; Associated with inherited retinal dystrophy.

What condition is associated with PDE6A p.Asp800= (c.2400C>T)?

PDE6A p.Asp800= (c.2400C>T) is associated with inherited retinal dystrophy, retinitis pigmentosa (ClinVar).

PDE6A p.Asp800=

Q: How common is PDE6A p.Asp800= (c.2400C>T) in the general population?

PDE6A p.Asp800= (c.2400C>T) is common (popmax 10.3%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2400C>T · rs4705390 · VCV138636

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 10.3%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

inherited retinal dystrophy

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 -4.5	GERP -5.4
Overall
CADD	0.585	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 10.3% Admixed American · 6,177/60,010 alleles

Filtering AF 10.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 9.99%

Overall 3.99% 64,370/1,613,876 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	10.3%	10
Finnishnot grpmax-eligible	6.45%	16
European (non-Finnish)	4%	25
South Asian	3.73%	27
Remaining individualsnot grpmax-eligible	3.61%	28
Middle Eastern	2.03%	49
Ashkenazi Jewishnot grpmax-eligible	1.86%	54
African / African-American	0.723%	138
Amishnot grpmax-eligible	0.329%	304
East Asian	0.0802%	1,246

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.Asp800=
Coding: c.2400C>T
MANE Select: NM_000440
dbSNP: rs4705390
Type: single nucleotide variant
Location: chr5:149863225 (GRCh38)
Gene constraint: LOEUF 0.888 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.80
Residue 800: the pdease domain

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

Disease context

inherited retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa

Similar variants

PDE6A p.Asp800Tyr Uncertain significance ★★ ⚠ same residue
PDE6A c.1065+2T>A Pathogenic/Likely pathogenic ★★ same condition
PDE6A c.1407+1G>C 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

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-asp800 (accessed [today's date]).

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