TACSTD2 p.Ala23=
c.69G>A · rs539258485 · VCV3052441
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0307%, amr)
Conditions
1
TACSTD2-related disorder
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 -0.49 | GERP -3.3 |
| Overall | ||
| CADD | 8.206 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0307%
Admixed American · 12/39,038 alleles
Filtering AF
0.0177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0139%
Overall
0.00218%
32/1,469,690 alleles · ultra-rare
exomes 13/1,317,494 · genomes 19/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0307% | 3,253 |
| African / African-American | 0.0251% | 3,979 |
| Remaining individualsnot grpmax-eligible | 0.00176% | 56,736 |
| European (non-Finnish) | 0.000179% | 559,726 |
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
- TACSTD2
- Protein
- p.Ala23=
- Coding
- c.69G>A
- MANE Select
- NM_002353
- dbSNP
- rs539258485
- Type
- single nucleotide variant
- Location
- chr1:58577088 (GRCh38)
- Gene constraint
- LOEUF 1.868 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.11 · 7 PDB
Disease context
TACSTD2-related disorder
Similar variants
- TACSTD2 p.Pro106= Likely benign same condition
- TACSTD2 c.-56C>G Uncertain significance ★★ same type
- TACSTD2 p.Arg135Leu Uncertain significance ★★ ⚠ same type
- TACSTD2 p.Gly276Asp Uncertain significance ★★ ⚠ same type
- TACSTD2 p.Gly59Ser Uncertain significance ★★ ⚠ same type
- TACSTD2 c.-169G>A Benign ★★ same type
- TACSTD2 c.-54A>C Benign ★★ same type
- TACSTD2 c.*202A>G Benign ★★ 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/tacstd2-p-ala23 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown