ALG1L2 p.Thr4=
c.12T>C · rs772308755 · VCV2654130
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0902%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Overall | ||
| CADD | 2.966 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0902%
European (non-Finnish) · 1,003/1,112,140 alleles
Filtering AF
0.0856%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0837%
Overall
0.07%
1,057/1,509,910 alleles · ultra-rare
exomes 1,006/1,358,768 · genomes 51/151,142 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0902% | 1,109 |
| Remaining individualsnot grpmax-eligible | 0.0818% | 1,223 |
| African / African-American | 0.00687% | 14,556 |
| Admixed American | 0.002% | 49,906 |
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
- ALG1L2
- Protein
- p.Thr4=
- Coding
- c.12T>C
- MANE Select
- NM_001136152
- dbSNP
- rs772308755
- Type
- single nucleotide variant
- Location
- chr3:130082028 (GRCh38)
- Gene constraint
- LOEUF 1.607 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.32
Similar variants
- ALG1L2 p.Ala173Thr Uncertain significance ★ ⚠ same type
- ALG1L2 p.Ala210Val Uncertain significance ★ ⚠ same type
- ALG1L2 p.Ala43Val Uncertain significance ★ ⚠ same type
- ALG1L2 p.Ala75Gly Uncertain significance ★ ⚠ same type
- ALG1L2 p.Arg115His Uncertain significance ★ ⚠ same type
- ALG1L2 p.Arg191Cys Uncertain significance ★ ⚠ same type
- ALG1L2 p.Arg191His Uncertain significance ★ ⚠ same type
- ALG1L2 p.Arg54Trp 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/alg1l2-p-thr4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown