ADGRA3 p.Ser318=
c.954T>A · rs199639027 · VCV1104732
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.078%, eas)
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 -1 | GERP -4.3 |
| Overall | ||
| CADD | 4.411 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.078%
East Asian · 35/44,858 alleles
Filtering AF
0.0576%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0506%
Overall
0.00235%
38/1,613,872 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.078% | 1,282 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,492 |
| South Asian | 0.0011% | 91,074 |
| European (non-Finnish) | 8.48e-05% | 1,179,825 |
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.Ser318=
- Coding
- c.954T>A
- MANE Select
- NM_145290
- dbSNP
- rs199639027
- Type
- single nucleotide variant
- Location
- chr4:22438387 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.20
- Residue 318
- the ig-like domain; a disulfide bond
Similar variants
- ADGRA3 p.Ser318Ala Uncertain significance ★★ ⚠ same residue
- 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
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-ser318 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown