Is IMPG2 p.Lys63fs (c.188_191del) pathogenic?

IMPG2 p.Lys63fs (c.188191del) is classified Pathogenic in IMPG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-01-09). No gnomAD frequency available for this variant; Associated with retinitis pigmentosa.

What condition is associated with IMPG2 p.Lys63fs (c.188_191del)?

IMPG2 p.Lys63fs (c.188_191del) is associated with retinitis pigmentosa (ClinVar).

How common is IMPG2 p.Lys63fs (c.188_191del) in the general population?

IMPG2 p.Lys63fs (c.188_191del) is no gnomAD frequency available for this variant (gnomAD).

How is Retinitis pigmentosa inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

IMPG2 p.Lys63fs

c.188_191del · rs2058802102 · VCV813050

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

retinitis pigmentosa

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 2 of 19
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.027	GERP -0.44

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: IMPG2
Protein: p.Lys63fs
Coding: c.188_191del
MANE Select: NM_016247
dbSNP: rs2058802102
Type: Deletion
Location: chr3:101319727 (GRCh38)
Gene constraint: LOEUF 0.773 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.28

Full IMPG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

IMPG2 c.533+4_533+7del Pathogenic ★ same condition
IMPG2 p.Ala1075fs Pathogenic ★ same condition
IMPG2 p.Ser212fs Pathogenic ★ same condition
IMPG2 p.Tyr349fs Pathogenic ★ same condition
IMPG2 p.Asn976fs Likely pathogenic same condition
IMPG2 c.3023-6_3030dup Pathogenic/Likely pathogenic ★★ same condition
IMPG2 p.Arg1088Ter Pathogenic/Likely pathogenic ★★ same condition
IMPG2 p.Trp758Ter 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/impg2-p-lys63fs (accessed [today's date]).

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