TACSTD2 p.His152=
c.456C>T · VCV3709558
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 3.1 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 10.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,824 alleles
Filtering AF
0.00267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00287%
46/1,601,766 alleles · very rare
exomes 46/1,449,428 · genomes 0/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,412 |
| European (non-Finnish) | 0.00356% | 28,072 |
| Admixed American | 0.00167% | 59,924 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,300 |
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.His152=
- Coding
- c.456C>T
- MANE Select
- NM_002353
- Type
- single nucleotide variant
- Location
- chr1:58576701 (GRCh38)
- Gene constraint
- LOEUF 1.868 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.11 · 7 PDB
- Residue 152
- a β-strand
Similar variants
- 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
- TACSTD2 c.*280T>C 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-his152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown