LAS1L p.Asp239=
c.717T>C · rs767354996 · VCV2711591
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00626%, nfe)
Conditions
1
Wilson-Turner syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.53 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.5 | GERP 1.7, phastCons 0.15 |
| Overall | ||
| CADD | 4.084 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00626%
European (non-Finnish) · 56/895,083 alleles
Filtering AF
0.00494%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00444%
Overall
0.00471%
57/1,209,548 alleles · very rare
exomes 54/1,098,128 · genomes 3/111,420 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00626% | 15,984 |
| Finnishnot grpmax-eligible | 0.00215% | 46,526 |
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
- LAS1L
- Protein
- p.Asp239=
- Coding
- c.717T>C
- MANE Select
- NM_031206
- dbSNP
- rs767354996
- Type
- single nucleotide variant
- Location
- chrX:65529676 (GRCh38)
- Structure
- AlphaFold pLDDT 63.26 · 5 PDB
- Residue 239
- the 'disordered' region
Similar variants
- LAS1L p.Asp239Tyr 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.Asp243Asn 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-asp239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown