USH2A p.Phe2996fs
c.8988del · VCV4849489
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
2
retinitis pigmentosa 39
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 45 of 72 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP -4, phastCons 0.088 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- USH2A
- Protein
- p.Phe2996fs
- Coding
- c.8988del
- MANE Select
- NM_206933
- Type
- Deletion
- Location
- chr1:215845891 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2996
- the fibronectin type-iii 16 domain
Disease context
retinitis pigmentosa 39 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: Usher syndrome type 2A
For Retinitis pigmentosa (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-5 / 10 000 (Europe)
Similar variants
- USH2A c.11389+1del Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.11549del Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.4251+1del Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.4758+1del Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.486-4_486-2del Likely pathogenic ★★ same condition
- USH2A c.7594+2del Likely pathogenic ★★ same condition
- USH2A c.9055+1del Pathogenic/Likely pathogenic ★★ same condition
- USH2A p.Ala1312fs 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/ush2a-p-phe2996fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown