LRIG2 p.Ala45=
c.135G>A · rs926368794 · VCV726805
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, 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 0.58 | GERP -0.69, phastCons 0.042 |
| Overall | ||
| CADD | 10.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,016 alleles
Overall
6.2e-05%
1/1,614,108 alleles · very rare
exomes 1/1,461,834 · genomes 0/152,274 · 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
- LRIG2
- Protein
- p.Ala45=
- Coding
- c.135G>A
- MANE Select
- NM_014813
- dbSNP
- rs926368794
- Type
- single nucleotide variant
- Location
- chr1:113073541 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87
- Residue 45
- the lrrnt domain
Similar variants
- LRIG2 p.Arg86Trp Uncertain significance ★★ ⚠ same type
- LRIG2 p.Glu11Ter Uncertain significance ★★ same type
- LRIG2 p.Lys245Arg Uncertain significance ★★ ⚠ same type
- LRIG2 c.2531-22G>A Benign ★★ same type
- LRIG2 p.Ala2= Likely benign ★★ same type
- LRIG2 p.Asp755Glu Benign ★★ same type
- LRIG2 p.Ile155Leu Likely benign ★★ same type
- LRIG2 p.Pro882Leu Likely benign ★★ 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/lrig2-p-ala45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown