ADGRV1 p.Pro5322=
c.15966T>C · rs772270681 · VCV1088562
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0275%, 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 -5.5 | GERP -3.3 |
| Overall | ||
| CADD | 0.439 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0275%
South Asian · 25/90,828 alleles
Filtering AF
0.019%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0163%
Overall
0.00212%
31/1,460,532 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0275% | 3,633 |
| Middle Eastern | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,229 |
| East Asian | 0.00223% | 44,872 |
| European (non-Finnish) | 0.00017% | 589,654 |
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
- ADGRV1
- Protein
- p.Pro5322=
- Coding
- c.15966T>C
- MANE Select
- NM_032119
- dbSNP
- rs772270681
- Type
- single nucleotide variant
- Location
- chr5:90811226 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Residue 5322
- the calx-beta 34 domain
Similar variants
- ADGRV1 c.10054-1G>T Pathogenic/Likely pathogenic ★★ same type
- ADGRV1 c.10974+1G>A Likely pathogenic ★★ same type
- ADGRV1 c.11581-2A>G Likely pathogenic ★★ same type
- ADGRV1 c.11757+2T>C Likely pathogenic ★★ same type
- ADGRV1 c.1239-1G>T Pathogenic/Likely pathogenic ★★ same type
- ADGRV1 c.13232-1G>A Pathogenic/Likely pathogenic ★★ same type
- ADGRV1 c.13654-2A>G Likely pathogenic ★★ same type
- ADGRV1 c.14972+1G>T Pathogenic/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/adgrv1-p-pro5322 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown