Is PDE6C p.Arg86Met (c.257G>T) pathogenic?

PDE6C p.Arg86Met (c.257G>T) is classified Uncertain significance in PDE6C (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). AlphaMissense: likely benign (0.2978); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with PDE6C p.Arg86Met (c.257G>T)?

PDE6C p.Arg86Met (c.257G>T) is associated with Inborn genetic diseases (ClinVar).

How common is PDE6C p.Arg86Met (c.257G>T) in the general population?

PDE6C p.Arg86Met (c.257G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about PDE6C p.Arg86Met (c.257G>T)?

AlphaMissense predicts likely benign (score 0.2978) — an in-silico prediction, not a clinical call.

PDE6C p.Arg86Met

c.257G>T · VCV3930103

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2978 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2978	likely benign
REVEL	0.439	indeterminate
SaProt	LLR -6.43	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.4	GERP -0.77, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 53 kb · p 8.6e-05 · regional, not allelic
Overall
CADD	23.7	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PDE6C
Protein: p.Arg86Met
Coding: c.257G>T
MANE Select: NM_006204
Type: single nucleotide variant
Location: chr10:93612982 (GRCh38)
Gene constraint: LOEUF 0.976 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 88.53 · 7 PDB
Residue 86: the gaf 1 domain; an α-helix

Full PDE6C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PDE6C p.Arg86= Likely benign ★ same residue
PDE6C p.Ala264Val Uncertain significance ★★ ⚠ same condition
PDE6C p.Ala462Val Uncertain significance ★★ ⚠ same condition
PDE6C p.Ala668Thr Uncertain significance ★★ ⚠ same condition
PDE6C p.Arg527Gln Uncertain significance ★★ ⚠ same condition
PDE6C p.Arg95Cys Uncertain significance ★★ ⚠ same condition
PDE6C p.Asn16Lys Uncertain significance ★★ ⚠ same condition
PDE6C p.Asn611Ser Uncertain significance ★★ ⚠ 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/pde6c-p-arg86met (accessed [today's date]).

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