ADGRA3 p.Phe706=
c.2118C>T · rs151265183 · VCV1158936
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0613%, afr)
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 -0.62 | GERP -5.6 |
| Overall | ||
| CADD | 7.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0613%
African / African-American · 46/75,018 alleles
Filtering AF
0.0472%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0422%
Overall
0.0052%
84/1,614,008 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0613% | 1,631 |
| South Asian | 0.0187% | 5,357 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,419 |
| Admixed American | 0.00667% | 15,001 |
| East Asian | 0.00223% | 44,874 |
| European (non-Finnish) | 0.000847% | 117,994 |
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.Phe706=
- Coding
- c.2118C>T
- MANE Select
- NM_145290
- dbSNP
- rs151265183
- Type
- single nucleotide variant
- Location
- chr4:22413296 (GRCh38)
- Gene constraint
- LOEUF 0.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.20
- Residue 706
- the gain-b domain; the 'gps' region
Similar variants
- ADGRA3 p.Ala1008Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala1120Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala1127Ser Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala177Val Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala26Pro Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala316Pro Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala37Gly Uncertain significance ★★ ⚠ same type
- ADGRA3 p.Ala407Thr Uncertain significance ★★ ⚠ 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/adgra3-p-phe706 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown