Is PRPH2 p.Val332fs (c.994del) pathogenic?

PRPH2 p.Val332fs (c.994del) is classified Pathogenic in PRPH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-14). No gnomAD frequency available for this variant; Associated with PRPH2-related disorder.

What condition is associated with PRPH2 p.Val332fs (c.994del)?

PRPH2 p.Val332fs (c.994del) is associated with PRPH2-related disorder (ClinVar).

How common is PRPH2 p.Val332fs (c.994del) in the general population?

PRPH2 p.Val332fs (c.994del) is no gnomAD frequency available for this variant (gnomAD).

PRPH2 p.Val332fs

c.994del · rs2152003792 · VCV1392728

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

PRPH2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1

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.Val332fs
Coding: c.994del
MANE Select: NM_000322
dbSNP: rs2152003792
Type: Deletion
Location: chr6:42698342 (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

PRPH2-related disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PRPH2 p.Val332Met Conflicting classifications of pathogenicity ★ same residue
PRPH2 p.Asn136fs Pathogenic/Likely pathogenic ★★ same condition
PRPH2 p.Asp50fs Pathogenic/Likely pathogenic ★★ same condition
PRPH2 p.Asp87fs Pathogenic ★★ same condition
PRPH2 p.Gln132fs Pathogenic ★★ same condition
PRPH2 p.Gly38fs Pathogenic ★★ same condition
PRPH2 p.Leu290fs Pathogenic ★★ same condition
PRPH2 p.Leu307fs 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/prph2-p-val332fs (accessed [today's date]).

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