USH1C p.Arg792=
c.2374C>A · rs200428926 · VCV751327
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0989%, sas)
Conditions
1
Usher syndrome type 1C
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -0.036, phastCons 0.18 |
| Overall | ||
| CADD | 3.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0989%
South Asian · 90/90,988 alleles
Filtering AF
0.0824%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0762%
Overall
0.00595%
96/1,613,344 alleles · ultra-rare
exomes 96/1,461,040 · genomes 0/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0989% | 1,011 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,474 |
| European (non-Finnish) | 0.000424% | 235,937 |
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
- USH1C
- Protein
- p.Arg792=
- Coding
- c.2374C>A
- MANE Select
- NM_153676
- dbSNP
- rs200428926
- Type
- single nucleotide variant
- Location
- chr11:17501057 (GRCh38)
- Gene constraint
- LOEUF 0.876 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 79.51 · 11 PDB
Similar variants
- USH1C p.Arg792Trp Uncertain significance ★★ ⚠ same residue
- USH1C p.Arg792Gln Uncertain significance ★★ ⚠ same residue
- USH1C p.Arg792Pro Uncertain significance ★ ⚠ same residue
- USH1C c.1020-2A>C Likely pathogenic ★★ same condition
- USH1C c.104+1G>A Pathogenic/Likely pathogenic ★★ same condition
- USH1C c.104+5G>C Likely pathogenic ★★ same condition
- USH1C c.2227-1G>T Pathogenic/Likely pathogenic ★★ same condition
- USH1C c.2280+2T>C 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/ush1c-p-arg792 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown