LRAT p.Ser194=
c.582T>C · rs1187117002 · VCV2194631
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, afr)
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 · T>G here scores Δ0.34 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.67 | GERP -5.7, phastCons 0.041 |
| Overall | ||
| CADD | 5.588 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,904 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000248%
4/1,613,720 alleles · very rare
exomes 3/1,461,598 · genomes 1/152,122 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,968 |
| European (non-Finnish) | 8.48e-05% | 1,179,778 |
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.Ser194=
- Coding
- c.582T>C
- MANE Select
- NM_004744
- dbSNP
- rs1187117002
- Type
- single nucleotide variant
- Location
- chr4:154749025 (GRCh38)
- Gene constraint
- LOEUF 1.214 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.69
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-ser194 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown