USH2A p.Thr1925=
c.5775A>T · VCV4937575
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
USH2A-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.3 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 18.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- USH2A
- Protein
- p.Thr1925=
- Coding
- c.5775A>T
- MANE Select
- NM_206933
- Type
- single nucleotide variant
- Location
- chr1:216073098 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 1925
- the fibronectin type-iii 5 domain
Similar variants
- USH2A c.10183-2A>G Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.10387+1G>A Likely pathogenic ★★ same condition
- USH2A c.11047+1G>A Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.11048-2A>G Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.11712-2A>G Likely pathogenic ★★ same condition
- USH2A c.14344-1G>T Pathogenic ★★ same condition
- USH2A c.14582+1G>C Pathogenic/Likely pathogenic ★★ same condition
- USH2A c.14791+2T>A 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-thr1925 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown