TXNL1 p.Leu165=
c.495G>C · rs145097903 · VCV730423
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.518%, afr)
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 -8.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.019 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.518%
African / African-American · 388/74,890 alleles
Filtering AF
0.476%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.459%
Overall
0.0268%
432/1,613,190 alleles · rare
exomes 193/1,461,212 · genomes 239/151,978 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.518% | 193 |
| Remaining individualsnot grpmax-eligible | 0.0448% | 2,231 |
| Admixed American | 0.0267% | 3,748 |
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
- TXNL1
- Protein
- p.Leu165=
- Coding
- c.495G>C
- MANE Select
- NM_004786
- dbSNP
- rs145097903
- Type
- single nucleotide variant
- Location
- chr18:56616312 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI 0.20 (gnomAD)
- Structure
- AlphaFold pLDDT 91.66 · 17 PDB
- Residue 165
- a β-strand; the pith domain
Similar variants
- TXNL1 c.563-4A>G Benign ★★ same type
- TXNL1 p.Ala25Thr Uncertain significance ★ ⚠ same type
- TXNL1 p.Arg259Lys Uncertain significance ★ ⚠ same type
- TXNL1 p.Asn114Ser Uncertain significance ★ ⚠ same type
- TXNL1 p.Asn276Tyr Uncertain significance ★ ⚠ same type
- TXNL1 p.Asp116Val Uncertain significance ★ ⚠ same type
- TXNL1 p.Asp147Glu Uncertain significance ★ ⚠ same type
- TXNL1 p.Asp223His 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/txnl1-p-leu165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown