ADGRV1 p.Pro4530=
c.13590C>A · rs41311745 · VCV1102478
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0627%, 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 -0.15 | GERP -1.2, phastCons 0.003 |
| Overall | ||
| CADD | 5.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0627%
African / African-American · 47/75,002 alleles
Filtering AF
0.0483%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0433%
Overall
0.00614%
99/1,612,700 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0627% | 1,596 |
| Middle Eastern | 0.0495% | 2,019 |
| Admixed American | 0.0217% | 4,602 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,937 |
| South Asian | 0.0022% | 45,401 |
| European (non-Finnish) | 0.00212% | 47,172 |
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.Pro4530=
- Coding
- c.13590C>A
- MANE Select
- NM_032119
- dbSNP
- rs41311745
- Type
- single nucleotide variant
- Location
- chr5:90783994 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Residue 4530
- the calx-beta 31 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-pro4530 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown