Is PRPH2 p.Val106fs (c.316_317del) pathogenic?

PRPH2 p.Val106fs (c.316317del) is classified Pathogenic in PRPH2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-01-17). No gnomAD frequency available for this variant; Associated with adult-onset foveomacular vitelliform dystrophy.

What condition is associated with PRPH2 p.Val106fs (c.316_317del)?

PRPH2 p.Val106fs (c.316_317del) is associated with adult-onset foveomacular vitelliform dystrophy (ClinVar).

How common is PRPH2 p.Val106fs (c.316_317del) in the general population?

PRPH2 p.Val106fs (c.316_317del) is no gnomAD frequency available for this variant (gnomAD).

How is Adult-onset foveomacular vitelliform dystrophy inherited?

Typically Autosomal dominant, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

PRPH2 p.Val106fs

c.316_317del · rs1562434117 · VCV599068

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

adult-onset foveomacular vitelliform dystrophy

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 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.12	GERP -3.1, phastCons 0.36

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: PRPH2
Protein: p.Val106fs
Coding: c.316_317del
MANE Select: NM_000322
dbSNP: rs1562434117
Type: Microsatellite
Location: chr6:42722018 (GRCh38)
Gene constraint: LOEUF 0.773 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.56 · 1 PDB

Full PRPH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

adult-onset foveomacular vitelliform dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Adult-onset foveomacular vitelliform dystrophy (Orphanet):

Inheritance: Autosomal dominant, Not applicable
Onset: Adult

Similar variants

PRPH2 p.Val106= Benign ★★ same residue
PRPH2 p.Glu302Ter Pathogenic/Likely pathogenic ★★ same condition
PRPH2 p.Ser212Thr Pathogenic/Likely pathogenic ★★ same condition
PRPH2 c.-166G>A Uncertain significance ★★ same condition
PRPH2 c.*592A>T Uncertain significance ★★ same condition
PRPH2 p.Glu162Lys Uncertain significance ★★ same condition
PRPH2 p.Glu56Gly Uncertain significance ★★ same condition
PRPH2 p.Gly31Val 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/prph2-p-val106fs (accessed [today's date]).

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