LRRC56 p.Pro240=
c.720G>A · rs571112595 · VCV1592517
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0741%, sas)
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 -4.4 | GERP -2.7 |
| Overall | ||
| CADD | 0.106 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0741%
South Asian · 62/83,674 alleles
Filtering AF
0.0593%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.054%
Overall
0.0126%
194/1,545,546 alleles · ultra-rare
exomes 176/1,393,662 · genomes 18/151,884 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0741% | 1,350 |
| Middle Eastern | 0.0503% | 1,990 |
| Remaining individualsnot grpmax-eligible | 0.0317% | 3,150 |
| Admixed American | 0.0138% | 7,248 |
| European (non-Finnish) | 0.00865% | 11,557 |
| African / African-American | 0.00549% | 18,229 |
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
- LRRC56
- Protein
- p.Pro240=
- Coding
- c.720G>A
- MANE Select
- NM_198075
- dbSNP
- rs571112595
- Type
- single nucleotide variant
- Location
- chr11:551226 (GRCh38)
- Gene constraint
- LOEUF 1.225 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 56.07
- Residue 240
- the lrrct domain
Similar variants
- LRRC56 p.Pro240Leu Uncertain significance ★ ⚠ same residue
- HRAS c.291-6T>G Benign ★★★ same type
- HRAS p.Gly12= Likely benign ★★★ same type
- LRRC56 p.Tyr53Ter Pathogenic/Likely pathogenic ★★ same type
- HRAS p.Arg68Gly Uncertain significance ★★ ⚠ same type
- HRAS p.Lys88Arg Uncertain significance ★★ ⚠ same type
- HRAS p.Met111Leu Uncertain significance ★★ same type
- HRAS p.Pro174Ala 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/lrrc56-p-pro240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown