LAS1L p.Arg464=
c.1392G>A · rs1238870516 · VCV1112575
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Wilson-Turner syndrome
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 -0.54 | GERP -0.67 |
| Overall | ||
| CADD | 6.901 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- LAS1L
- Protein
- p.Arg464=
- Coding
- c.1392G>A
- MANE Select
- NM_031206
- dbSNP
- rs1238870516
- Type
- single nucleotide variant
- Location
- chrX:65523616 (GRCh38)
- Structure
- AlphaFold pLDDT 63.26 · 5 PDB
Similar variants
- LAS1L p.Arg464Gln Uncertain significance ★ ⚠ same residue
- LAS1L p.Arg415Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- LAS1L p.Gly413Arg Pathogenic/Likely pathogenic ★★ ⚠ same condition
- LAS1L p.Arg624Lys Uncertain significance ★★ ⚠ same condition
- LAS1L p.Arg654Leu Uncertain significance ★★ ⚠ same condition
- LAS1L p.Arg684Gln Uncertain significance ★★ ⚠ same condition
- LAS1L p.Asp221Glu Uncertain significance ★★ ⚠ same condition
- LAS1L p.Asp239Tyr Uncertain significance ★★ ⚠ same condition
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/las1l-p-arg464 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown