ADGRL2 p.Asn342=
c.1026C>T · rs149165038 · VCV2638900
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.103%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.352 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -3.5 |
| Overall | ||
| CADD | 1.002 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.103%
European (non-Finnish) · 1,219/1,179,746 alleles
Filtering AF
0.0984%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0965%
Overall
0.0803%
1,296/1,613,744 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.103% | 968 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| Finnishnot grpmax-eligible | 0.0203% | 4,925 |
| Admixed American | 0.02% | 4,995 |
| African / African-American | 0.0133% | 7,500 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,799 |
| South Asian | 0.00549% | 18,217 |
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
- ADGRL2
- Protein
- p.Asn342=
- Coding
- c.1026C>T
- MANE Select
- NM_001366006
- dbSNP
- rs149165038
- Type
- single nucleotide variant
- Location
- chr1:81943585 (GRCh38)
- Gene constraint
- LOEUF 0.301 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 69.66 · 1 PDB
- Residue 342
- the olfactomedin-like domain
Similar variants
- ADGRL2 p.Lys555Arg Likely benign ★★ same type
- ADGRL2 p.Thr1294= Benign ★★ same type
- ADGRL2 p.Ala1070Thr Uncertain significance ★ ⚠ same type
- ADGRL2 p.Ala1090Val Uncertain significance ★ ⚠ same type
- ADGRL2 p.Ala160Val Uncertain significance ★ ⚠ same type
- ADGRL2 p.Ala170Val Uncertain significance ★ ⚠ same type
- ADGRL2 p.Ala191Ser Uncertain significance ★ ⚠ same type
- ADGRL2 p.Ala29Val 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/adgrl2-p-asn342 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown