LRRC56 p.Val481=
c.1443C>T · rs144961654 · VCV1528306
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0168%, amr)
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 0.78 | GERP -0.091, phastCons 0.69 |
| Overall | ||
| CADD | 3.325 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0168%
Admixed American · 10/59,656 alleles
Filtering AF
0.00905%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00685%
Overall
0.0069%
111/1,607,810 alleles · ultra-rare
exomes 108/1,455,666 · genomes 3/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0168% | 5,966 |
| European (non-Finnish) | 0.00823% | 12,151 |
| Remaining individualsnot grpmax-eligible | 0.00642% | 15,584 |
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.Val481=
- Coding
- c.1443C>T
- MANE Select
- NM_198075
- dbSNP
- rs144961654
- Type
- single nucleotide variant
- Location
- chr11:554090 (GRCh38)
- Gene constraint
- LOEUF 1.225 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 56.07
- Residue 481
- a UniProt-annotated variant site (in cild39)
Similar variants
- 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
- HRAS p.Pro179Leu 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-val481 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown