ADGRA3 p.Thr286=
c.858C>T · rs35762546 · VCV1165990
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.34%, mid)
Conditions
1
inherited retinal dystrophy
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 -3.2 | GERP -4 |
| Overall | ||
| CADD | 2.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.34%
Middle Eastern · 263/6,054 alleles
Filtering AF
3.91%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.75%
Overall
1.63%
26,299/1,613,086 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 4.34% | 23 |
| East Asian | 2.26% | 44 |
| Finnishnot grpmax-eligible | 2.19% | 46 |
| Remaining individualsnot grpmax-eligible | 1.87% | 53 |
| European (non-Finnish) | 1.65% | 60 |
| Admixed American | 1.55% | 65 |
| Amishnot grpmax-eligible | 1.43% | 70 |
| Ashkenazi Jewishnot grpmax-eligible | 1.25% | 80 |
| South Asian | 1.15% | 87 |
| African / African-American | 0.785% | 127 |
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
- ADGRA3
- Protein
- p.Thr286=
- Coding
- c.858C>T
- MANE Select
- NM_145290
- dbSNP
- rs35762546
- Type
- single nucleotide variant
- Location
- chr4:22442712 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.20
- Residue 286
- the ig-like domain; a disulfide bond
Similar variants
- ADGRA3 p.Arg1163Gln Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Arg157Gln Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Arg525Trp Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Gly1303Cys Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Gly1303Ser Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Gly57Ser Uncertain significance ★★ ⚠ same condition
- ADGRA3 p.Leu798Phe Uncertain significance ★★ same condition
- ADGRA3 p.Met1147Thr Uncertain significance ★★ ⚠ 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/adgra3-p-thr286 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown