ADGRG2 p.Val620=
c.1860G>C · rs1265451853 · VCV2660119
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00317%, nfe)
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 0.89 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 1.128 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00317%
European (non-Finnish) · 28/881,988 alleles
Filtering AF
0.0022%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00189%
Overall
0.00235%
28/1,193,239 alleles · very rare
exomes 27/1,081,226 · genomes 1/112,013 · joint denominator
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
- ADGRG2
- Protein
- p.Val620=
- Coding
- c.1860G>C
- MANE Select
- NM_001079858
- dbSNP
- rs1265451853
- Type
- single nucleotide variant
- Location
- chrX:19004859 (GRCh38)
- Structure
- AlphaFold pLDDT 62.76
- Residue 620
- a UniProt-annotated variant site (in cbavdx; the protein is undetectable); a UniProt-annotated variant site (in cbavdx; uncertain significance)
Similar variants
- ADGRG2 c.710+4T>C Benign ★★ same type
- ADGRG2 p.Asn771Ser Benign ★★ same type
- ADGRG2 p.His290Gln Benign ★★ same type
- ADGRG2 p.Arg825Ter Pathogenic ★ same type
- ADGRG2 p.Ser84Ter Pathogenic ★ same type
- ADGRG2 c.119-4A>G Uncertain significance ★ same type
- ADGRG2 p.Ala670Thr Uncertain significance ★ ⚠ same type
- ADGRG2 p.Ala686Thr 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/adgrg2-p-val620 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown