CSTB p.Ala12=
c.36C>T · rs2123387876 · VCV1179990
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,529,694)
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 6.2 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 14.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,529,694). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CSTB
- Protein
- p.Ala12=
- Coding
- c.36C>T
- MANE Select
- NM_000100
- dbSNP
- rs2123387876
- Type
- single nucleotide variant
- Location
- chr21:43776234 (GRCh38)
- Gene constraint
- LOEUF 1.681 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 95.81 · 3 PDB
Similar variants
- CSTB p.Ala12Thr Uncertain significance ★ ⚠ same residue
- CSTB c.67-1G>C Pathogenic ★★ same type
- CSTB p.Arg68Ter Pathogenic ★★ same type
- CSTB p.Gln22Ter Pathogenic/Likely pathogenic ★★ same type
- CSTB p.Gln46Ter Pathogenic/Likely pathogenic ★★ same type
- CSTB p.Ala49Thr Uncertain significance ★★ ⚠ same type
- CSTB p.Ala90Thr Uncertain significance ★★ ⚠ same type
- CSTB p.Asn52Ile 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/cstb-p-ala12 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown