LIPH p.Ile151=
c.453C>T · rs563060609 · VCV2886020
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0579%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.22 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -3.7, phastCons 0.99 |
| Overall | ||
| CADD | 9.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0579%
East Asian · 26/44,870 alleles
Filtering AF
0.0405%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0347%
Overall
0.00297%
48/1,613,774 alleles · ultra-rare
exomes 39/1,461,552 · genomes 9/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0579% | 1,726 |
| African / African-American | 0.00933% | 10,719 |
| South Asian | 0.00439% | 22,769 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,247 |
| European (non-Finnish) | 0.000763% | 131,081 |
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
- LIPH
- Protein
- p.Ile151=
- Coding
- c.453C>T
- MANE Select
- NM_139248
- dbSNP
- rs563060609
- Type
- single nucleotide variant
- Location
- chr3:185533644 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.89
Similar variants
- LIPH p.Arg110Ter Pathogenic/Likely pathogenic ★★ same type
- LIPH p.Cys246Ser Pathogenic/Likely pathogenic ★★ same type
- LIPH p.His248Asn Pathogenic/Likely pathogenic ★★ same type
- LIPH p.Ala180Gly Uncertain significance ★★ ⚠ same type
- LIPH p.Arg110Leu Uncertain significance ★★ ⚠ same type
- LIPH p.Ile336Met Uncertain significance ★★ ⚠ same type
- LIPH p.Thr286Met Uncertain significance ★★ ⚠ same type
- LIPH c.1094+29C>T Benign ★★ 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/liph-p-ile151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown