LIMA1 p.Pro79=
c.237A>G · rs528872075 · VCV3060422
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.27%, amr)
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 -4.5 | GERP -3.2 |
| Overall | ||
| CADD | 3.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.27%
Admixed American · 760/60,010 alleles
Filtering AF
1.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.16%
Overall
0.0488%
788/1,614,194 alleles · low-frequency
exomes 669/1,461,890 · genomes 119/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.27% | 79 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| African / African-American | 0.00933% | 10,721 |
| European (non-Finnish) | 0.000678% | 147,504 |
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
- LIMA1
- Protein
- p.Pro79=
- Coding
- c.237A>G
- MANE Select
- NM_016357
- dbSNP
- rs528872075
- Type
- single nucleotide variant
- Location
- chr12:50222414 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 52.12 · 1 PDB
- Residue 79
- the 'disordered' region
Similar variants
- LIMA1 p.Ala113Gly Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala136Val Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala183Asp Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala214Ser Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala367Val Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala479Val Uncertain significance ★ ⚠ same type
- LIMA1 p.Ala531Thr Uncertain significance ★ ⚠ same type
- LIMA1 p.Arg141Gln 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/lima1-p-pro79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown