ALG10 p.Thr134=
c.402A>C · rs77450248 · VCV785400
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4%, afr)
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 -0.6 | GERP -1.2 |
| Overall | ||
| CADD | 1.828 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4%
African / African-American · 3,004/75,026 alleles
Filtering AF
3.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.84%
Overall
0.239%
3,854/1,614,004 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 0.895% | 112 |
| Middle Eastern | 0.528% | 189 |
| Admixed American | 0.338% | 296 |
| Remaining individualsnot grpmax-eligible | 0.323% | 309 |
| European (non-Finnish) | 0.012% | 8,368 |
| South Asian | 0.00769% | 13,012 |
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
- ALG10
- Protein
- p.Thr134=
- Coding
- c.402A>C
- MANE Select
- NM_032834
- dbSNP
- rs77450248
- Type
- single nucleotide variant
- Location
- chr12:34025895 (GRCh38)
- Gene constraint
- LOEUF 0.901 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.51
Similar variants
- ALG10 p.Thr134Ile Uncertain significance ★ ⚠ same residue
- ALG10 p.Ser243= Benign ★★ same type
- ALG10 p.Val269Ile Benign ★★ same type
- ALG10 c.369+1G>T Likely pathogenic ★ same type
- ALG10 p.Met61Val Likely pathogenic ★ ⚠ same type
- ALG10 p.Ala11Asp Uncertain significance ★ ⚠ same type
- ALG10 p.Ala11Thr Uncertain significance ★ ⚠ same type
- ALG10 p.Ala125Thr 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/alg10-p-thr134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown