Is PDE6B p.Val835= (c.2505A>G) pathogenic?

PDE6B p.Val835= (c.2505A>G) is classified Benign/Likely benign in PDE6B (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-02). Low-frequency (popmax 3.06%, afr); Associated with congenital stationary night blindness autosomal dominant 2.

How common is PDE6B p.Val835= (c.2505A>G) in the general population?

PDE6B p.Val835= (c.2505A>G) is low-frequency (popmax 3.06%, afr) (gnomAD).

PDE6B p.Val835=

Q: What condition is associated with PDE6B p.Val835= (c.2505A>G)?

PDE6B p.Val835= (c.2505A>G) is associated with congenital stationary night blindness autosomal dominant 2, retinitis pigmentosa (ClinVar).

c.2505A>G · rs61734864 · VCV349397

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.06%, afr)

Conditions

congenital stationary night blindness autosomal dominant 2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.015	strongly benign-leaning
Splicing
SpliceAI	Δ0.52	acceptor loss, 2 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -1	GERP -2.9
Overall
CADD	1.972	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.06% African / African-American · 2,294/74,942 alleles

Filtering AF 2.96% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.91%

Overall 0.161% 2,594/1,612,238 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.06%	33
Remaining individualsnot grpmax-eligible	0.247%	405
Admixed American	0.198%	504
Middle Eastern	0.0333%	3,003
South Asian	0.00439%	22,766
European (non-Finnish)	0.00178%	56,134

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: PDE6B
Protein: p.Val835=
Coding: c.2505A>G
MANE Select: NM_000283
dbSNP: rs61734864
Type: single nucleotide variant
Location: chr4:670047 (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

congenital stationary night blindness autosomal dominant 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa

Similar variants

PDE6B c.1060-1G>T Pathogenic/Likely pathogenic ★★ same condition
PDE6B c.1107+3A>G Pathogenic/Likely pathogenic ★★ same condition
PDE6B c.1832+1G>T Pathogenic ★★ same condition
PDE6B c.1921-9C>G Pathogenic ★★ same condition
PDE6B c.2021+2T>G Pathogenic/Likely pathogenic ★★ same condition
PDE6B c.2193+1G>A Pathogenic ★★ same condition
PDE6B p.Arg560Cys Pathogenic/Likely pathogenic ★★ same condition
PDE6B p.Asp600Asn 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/pde6b-p-val835 (accessed [today's date]).

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