LRIG2 p.Ala2=
c.6G>C · rs140301079 · VCV714080
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.1%, mid)
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 11 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 15.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.1%
Middle Eastern · 188/6,056 alleles
Filtering AF
2.74%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.6%
Overall
0.0718%
1,158/1,613,456 alleles · low-frequency
exomes 1,063/1,461,114 · genomes 95/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 3.1% | 32 |
| Ashkenazi Jewishnot grpmax-eligible | 0.785% | 127 |
| Remaining individualsnot grpmax-eligible | 0.15% | 665 |
| Admixed American | 0.128% | 778 |
| South Asian | 0.0659% | 1,517 |
| European (non-Finnish) | 0.042% | 2,383 |
| African / African-American | 0.0147% | 6,823 |
| East Asian | 0.00223% | 44,870 |
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.Ala2=
- Coding
- c.6G>C
- MANE Select
- NM_014813
- dbSNP
- rs140301079
- Type
- single nucleotide variant
- Location
- chr1:113073412 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87
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.Asp755Glu Benign ★★ same type
- LRIG2 p.Ile155Leu Likely benign ★★ same type
- LRIG2 p.Pro882Leu Likely benign ★★ same type
- LRIG2 p.Ser563Thr 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-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown