LIPH p.Ala267=
c.801G>A · VCV4749544
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.106 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,052 alleles
Filtering AF
0.00367%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00329%
Overall
0.00409%
66/1,612,304 alleles · very rare
exomes 63/1,460,210 · genomes 3/152,094 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,007 |
| European (non-Finnish) | 0.00467% | 21,427 |
| East Asian | 0.00446% | 22,440 |
| Admixed American | 0.00167% | 59,990 |
| African / African-American | 0.00134% | 74,854 |
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.Ala267=
- Coding
- c.801G>A
- MANE Select
- NM_139248
- Type
- single nucleotide variant
- Location
- chr3:185519227 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.89
- Residue 267
- a UniProt-annotated variant site (in arwh2)
Similar variants
- LIPH p.Ala267Glu Uncertain significance ★ ⚠ same residue
- 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
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-ala267 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown