LRAT p.Phe164=
c.492C>T · rs915089130 · VCV1540123
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, 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 -1.9 | |
| Overall | ||
| CADD | 9.901 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,078 alleles
Overall
6.2e-05%
1/1,613,822 alleles · very rare
exomes 0/1,461,768 · genomes 1/152,054 · 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
- LRAT
- Protein
- p.Phe164=
- Coding
- c.492C>T
- MANE Select
- NM_004744
- dbSNP
- rs915089130
- Type
- single nucleotide variant
- Location
- chr4:154744818 (GRCh38)
- Gene constraint
- LOEUF 1.214 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.69
- Residue 164
- the lrat domain
Similar variants
- LRAT p.Arg47Ter Pathogenic/Likely pathogenic ★★ same type
- LRAT p.Arg55Gly Pathogenic/Likely pathogenic ★★ same type
- LRAT p.Arg55Trp Pathogenic ★★ same type
- LRAT p.Cys168Ter Pathogenic ★★ same type
- LRAT p.Leu157Pro Likely pathogenic ★★ same type
- LRAT c.*2625A>G Uncertain significance ★★ same type
- LRAT p.Ala120Gly Uncertain significance ★★ ⚠ same type
- LRAT p.Ala30Val 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/lrat-p-phe164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown