USH2A p.Pro3801=
c.11403C>T · rs775502523 · VCV1132861
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00441%, sas)
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 0.96 | GERP -1.7, phastCons 0.4 |
| Overall | ||
| CADD | 6.431 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00441%
South Asian · 4/90,662 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000894%
Overall
0.00125%
20/1,599,820 alleles · very rare
exomes 18/1,453,460 · genomes 2/146,360 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00441% | 22,666 |
| Admixed American | 0.00171% | 58,526 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,864 |
| African / African-American | 0.00137% | 73,078 |
| European (non-Finnish) | 0.00111% | 90,289 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- USH2A
- Protein
- p.Pro3801=
- Coding
- c.11403C>T
- MANE Select
- NM_206933
- dbSNP
- rs775502523
- Type
- single nucleotide variant
- Location
- chr1:215743322 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 3801
- the fibronectin type-iii 23 domain
Similar variants
- USH2A c.12295-3T>A Pathogenic ★★★ same type
- USH2A c.8559-2A>G Pathogenic ★★★ same type
- USH2A c.8682-9A>G Pathogenic ★★★ same type
- USH2A p.Ala4740Asp Pathogenic ★★★ ⚠ same type
- USH2A p.Arg3905Cys Pathogenic ★★★ ⚠ same type
- USH2A p.Arg4192Cys Likely pathogenic ★★★ ⚠ same type
- USH2A p.Asn346His Pathogenic ★★★ same type
- USH2A p.Asn4292Asp 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-pro3801 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown