ADGRV1 p.Pro4445=
c.13335C>T · rs573984372 · VCV1915536
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, 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 -3.8 | GERP -3.9 |
| Overall | ||
| CADD | 5.029 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,996 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00065%
Overall
0.00143%
23/1,613,532 alleles · very rare
exomes 17/1,461,322 · genomes 6/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,999 |
| East Asian | 0.00223% | 44,870 |
| Admixed American | 0.00167% | 59,982 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| European (non-Finnish) | 0.00136% | 73,723 |
| South Asian | 0.0011% | 91,080 |
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.Pro4445=
- Coding
- c.13335C>T
- MANE Select
- NM_032119
- dbSNP
- rs573984372
- Type
- single nucleotide variant
- Location
- chr5:90783227 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Residue 4445
- the calx-beta 30 domain
Similar variants
- ADGRV1 p.Pro4445Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- ADGRV1 p.Pro4445Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro4445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown