LIPG p.Ser4=
c.12C>A · rs874565 · VCV1635172
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 12.6%, afr) — too common for a highly-penetrant pathogenic allele
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 -7.7 | GERP -3.2 |
| Overall | ||
| CADD | 2.488 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
12.6%
African / African-American · 9,439/74,954 alleles
Filtering AF
12.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 12.3%
Overall
0.659%
10,629/1,613,182 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 12.6% | 8 |
| Admixed American | 0.833% | 120 |
| Remaining individualsnot grpmax-eligible | 0.775% | 129 |
| Middle Eastern | 0.333% | 300 |
| South Asian | 0.0253% | 3,958 |
| European (non-Finnish) | 0.0139% | 7,195 |
| Finnishnot grpmax-eligible | 0.00156% | 63,952 |
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.Ser4=
- Coding
- c.12C>A
- MANE Select
- NM_006033
- dbSNP
- rs874565
- Type
- single nucleotide variant
- Location
- chr18:49562320 (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-ser4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown