LRIG2 p.Ser163=
c.489A>G · VCV3344535
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 15.9%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -0.89, phastCons 1 |
| Overall | ||
| CADD | 9.324 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.9%
African / African-American · 11,693/73,346 alleles
Filtering AF
15.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.6%
Overall
0.844%
13,376/1,584,488 alleles · common
exomes 6,550/1,436,500 · genomes 6,826/147,988 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 15.9% | 6 |
| Admixed American | 1.2% | 83 |
| Remaining individualsnot grpmax-eligible | 1.13% | 88 |
| Middle Eastern | 0.645% | 155 |
| South Asian | 0.0452% | 2,213 |
| European (non-Finnish) | 0.0185% | 5,409 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00698% | 14,330 |
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.Ser163=
- Coding
- c.489A>G
- MANE Select
- NM_014813
- Type
- single nucleotide variant
- Location
- chr1:113093538 (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.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-ser163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown