LIPG p.Ala172=
c.516G>A · VCV4699203
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0231%, sas)
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 -2.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.517 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0231%
South Asian · 21/91,082 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0129%
Overall
0.00142%
23/1,614,176 alleles · ultra-rare
exomes 22/1,461,874 · genomes 1/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0231% | 4,337 |
| East Asian | 0.00223% | 44,880 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
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
- LIPG
- Protein
- p.Ala172=
- Coding
- c.516G>A
- MANE Select
- NM_006033
- Type
- single nucleotide variant
- Location
- chr18:49569493 (GRCh38)
- Gene constraint
- LOEUF 0.883 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.76
Similar variants
- LIPG p.Arg112Gly Uncertain significance ★★ ⚠ same type
- LIPG p.Arg224Cys Uncertain significance ★★ ⚠ same type
- LIPG p.Arg302Cys Uncertain significance ★★ ⚠ same type
- LIPG p.Arg431Cys Uncertain significance ★★ ⚠ same type
- LIPG p.Arg448His Uncertain significance ★★ ⚠ same type
- LIPG p.Arg484Gln Uncertain significance ★★ ⚠ same type
- LIPG p.Asn439Ser Uncertain significance ★★ ⚠ same type
- LIPG p.Asn80Ser 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/lipg-p-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown