LRIG2 p.Asp760=
c.2280T>C · rs759266921 · VCV3041045
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
Conditions
1
LRIG2-related disorder
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 0.96 | GERP -0.84, phastCons 1 |
| Overall | ||
| CADD | 7.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,180,026 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00062%
10/1,614,008 alleles · very rare
exomes 8/1,461,884 · genomes 2/152,124 · 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.Asp760=
- Coding
- c.2280T>C
- MANE Select
- NM_014813
- dbSNP
- rs759266921
- Type
- single nucleotide variant
- Location
- chr1:113114626 (GRCh38)
- Gene constraint
- LOEUF 0.95 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.87
- Residue 760
- the ig-like c2-type 3 domain
Disease context
LRIG2-related disorder
Similar variants
- LRIG2 c.660-7G>A Likely benign same condition
- LRIG2 p.Asp928= Likely benign same condition
- LRIG2 p.Phe187= Likely benign same condition
- LRIG2 p.Thr765Ile Benign same condition
- 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
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-asp760 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown