LAS1L p.Phe714=
c.2142C>T · VCV3384841
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00172%, nfe)
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 -0.018 | GERP -3.1, phastCons 0.75 |
| Overall | ||
| CADD | 6.187 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00172%
European (non-Finnish) · 15/872,738 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000818%
Overall
0.00129%
15/1,166,318 alleles · very rare
exomes 14/1,054,053 · genomes 1/112,265 · 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
- LAS1L
- Protein
- p.Phe714=
- Coding
- c.2142C>T
- MANE Select
- NM_031206
- Type
- single nucleotide variant
- Location
- chrX:65512838 (GRCh38)
- Structure
- AlphaFold pLDDT 63.26 · 5 PDB
Similar variants
- LAS1L p.Arg415Trp Pathogenic/Likely pathogenic ★★ ⚠ same type
- LAS1L p.Gly413Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- LAS1L p.Arg624Lys Uncertain significance ★★ ⚠ same type
- LAS1L p.Arg654Leu Uncertain significance ★★ ⚠ same type
- LAS1L p.Arg684Gln Uncertain significance ★★ ⚠ same type
- LAS1L p.Asp221Glu Uncertain significance ★★ ⚠ same type
- LAS1L p.Asp239Tyr Uncertain significance ★★ ⚠ same type
- LAS1L p.Asp243Asn 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/las1l-p-phe714 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown