USH2A p.Pro4601fs
c.13802del · VCV3645670
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 63 of 72 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -3.6 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- USH2A
- Protein
- p.Pro4601fs
- Coding
- c.13802del
- MANE Select
- NM_206933
- Type
- Deletion
- Location
- chr1:215674109 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 4601
- the fibronectin type-iii 31 domain
Similar variants
- USH2A p.Pro4601Leu Uncertain significance ★★ ⚠ same residue
- USH2A p.Pro4601= Likely benign ★★ same residue
- USH2A p.Pro4601Ala Uncertain significance same residue
- USH2A c.12295-?_14133+?del Likely pathogenic ★★★ same type
- USH2A c.11389+1del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.11549del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.4251+1del Pathogenic/Likely pathogenic ★★ same type
- USH2A c.4758+1del Pathogenic/Likely pathogenic ★★ same type
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-pro4601fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown