TEX10 p.Ala447=
c.1341G>A · VCV3806134
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 11.55 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,986 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00186%
30/1,613,990 alleles · ultra-rare
exomes 25/1,461,810 · genomes 5/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,665 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,802 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| European (non-Finnish) | 0.00153% | 65,556 |
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
- TEX10
- Protein
- p.Ala447=
- Coding
- c.1341G>A
- MANE Select
- NM_017746
- Type
- single nucleotide variant
- Location
- chr9:100330079 (GRCh38)
- Gene constraint
- LOEUF 0.35 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.04 · 4 PDB
- Residue 447
- an α-helix
Similar variants
- TEX10 p.Ala112Thr Uncertain significance ★ ⚠ same type
- TEX10 p.Ala273Thr Uncertain significance ★ ⚠ same type
- TEX10 p.Ala651Thr Uncertain significance ★ ⚠ same type
- TEX10 p.Arg178His Uncertain significance ★ ⚠ same type
- TEX10 p.Arg350Gln Uncertain significance ★ ⚠ same type
- TEX10 p.Arg550Cys Uncertain significance ★ ⚠ same type
- TEX10 p.Arg703Gln Uncertain significance ★ ⚠ same type
- TEX10 p.Arg7Cys 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/tex10-p-ala447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown